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Basically MTB and road bikes have different brand parts (like deore / XT; Sora / Utegra etc).
What are the main differences between the 2 types, that will make it incompatible?
Are there things that do differ, but not affecting the whole system, so I can change only one of them to improve my commute?
I think this is quite a broad question, so I'll highlight a few parts of the bike:
Seatposts/saddles: Probably interchangable
Forks: You wouldn't want to swap them, and chances are a beefy mountain fork wouldn't go into a road frame anyway, even if you could get the right headset.
Gearing: Road bikes typically have higher gearing than mountain bikes
There are larger chainrings on the crankset on a road bike - typically 52/39 or something or a 50/34 versus a big ring in the low 40s or 30s on a mountain bike.
The rear cassette is often smaller on a road bike as well (you won't see a 36t big rear cog on many road bikes, unless they're touring bikes).
Front derailleurs: FD's need to be shaped to the number of chainrings (typically 2, less so common 3 on a road bike vs often 3 on a mountain bike) as well as the size of the chainrings. For this reason (and in some cases the amount of cable pull needed to move the front derailleur) you can't mix road cranksets with mountain front derailleurs and mountain cranksets with road front derailleurs. On a mountain frame, you probably can't clear a road double if you were to mount it on, and you may have derailleur mounting issues when putting a mountain crankset on a road frame in some cases.
Rear derailleurs: Until 10 speed, you could swap them around when you stuck within the brand (then they introduced different cable pulls introducing shifter incompatibilites, so road shifters have to be paired with road derailleurs and similarly for mountain). The mountain rear derailleurs can shift larger rear cogs than road ones.
Cassettes: You can interchange them if you want in a lot of cases (touring road bikes often use big rear cogs).
Shifters: The front derailleur needs to be matched to road/mountain shifter. Rear derailleur will need to be matched if >=10 speed. Friction shifters always work.
Wheels: Mountain rims are often wider to support wider tires at lower pressures and are usually built to be more robust. Your hub widths are often the same, but mountain axles can cause compatibility issues (not just your usual QR) with different frames. Note 700c = 29". Often wheels built for tougher road riding (e.g. touring) use mountain bike hubs.
Tires: Mountain tires are typically fatter than road tires.
Cables/Cable Housings: You can use the same types.
Handlebars: Mountain and Road bars have different diameters, so brake levers and shifters designed for one will not fit on the other.
Brakes: Typically, road brakes (mechanical disc brakes for road, caliper brakes, cantilever brakes) are short pull while mountain brakes are often long pull (v-brakes, mechanical disc brakes). This means you require a travel agent or special levers to run v-brakes or certain mechanical disc brakes on a road bike. Hydraulic systems are quite new on road bikes. Since you can't mount the levers onto a mountain bar, exchanging them is somewhat moot at this point.
Racks+fenders: These are wheel size and disc/not disc specific. Read the directions on the rack+fenders.
Generally, road stuff is lighter than mountain stuff. Probably less durable in a crash though.
Now to part 2 of the question: What can you change on a bike to improve your commute? This question has been asked on SE a bunch of times, but typically the answer for commuting on a mountain bike is to lock out your suspension if you can (or switch to a rigid fork) and fit slick tires. You could also try a smaller cassette if you want, but other than that, you're going to want to get a new bike. If you have a road bike, you sometimes will want to fit a big cassette so you have lower gears available (you may need a new chain, and to make sure all the capacities of the derailleurs are within spec, else you may need a new rear derailleur) and bigger tires to make things more comfortable.
The main differences to the drive train is the length of the rear derailleur arm. MTBs have lower and wider spaced gearing which means the rear derailleur has to handle a bigger span in chain length.
A MTB typically has a large chainring with 42 teeth and a small one with 22 and a rear cassette with 12 - 28 tooth span - so the chain has to fit both a 42+28 combo and a 22+12 combo. That makes for a span of 70 - 34 = 36 teeth.
On a typical road bike, the biggest combo is 52+22 and the smallest is 42+11, thus a span of 72 - 53 = 19 teeth.
In order to keep the chain tight, the derailleur has to be able to "suck up" 17 more chain links on a MTB, which is why it has a longer arm.
Main difference is tooth count, and that imposes differences in derailleur dimensions.
As other answer mentions, gear range is wider in a MTB, so the rear derailleur has to be able to take-up more chain slack. A longer cage solves this. As long as they are designed with the same cable pull ratio, they are compatible, you can easily fit an MTB derailleur to a road frame.
Front derailleur are sized accordingly to the chainring and whether the crankset is double or triple. Chainring count and size determine derailleur cage shape and clamp height relative to bottom bracket. One size is not compatible with the other, I know from experience. Some combinations may be made to work, but you have to fiddle a lot, and maybe modify some parts. I don't think it's worth it. Some frames may not allow a different derailleur to be installed high or low enough.
Rear derailleur on the other hand are more cross compatible. I have seen MTB derailleurs and cassettes on road frames but I don't remember precisely what shifter where they using.
In my case, I have a Shimano Sora road derailleur on a DH bike with an 8 speed SRAM11-28 cassette, controlled by a Microshift shifter. Sure the cassette is wider than usual for a Sora derailleur, but the DH bike has only one chainring, so no tooth difference problems arose.
In another case, I have an old road bike that came with a 6 speed 12-22 freewheel that I replaced with a 6 speed 12-28 while keeping the rear derailleur. However, I did not change the chain so I can't use the big chainring with all the rear gears yet. This bike uses friction shifters.
If you want to improve your commute by changing drivetrain parts, I would first ask if you spend a lot of time in the lowest gear or if there are climbs in your commute that are close to impossible with the gears you have. If the answer is yes, then put in an MTB cassette with a medium cage MTB derailleur. Just verify that for your rear gear count the shifters and deraileurs have the same cable pull ratio.
Second option would be a compact road crankset and maybe a different front derailleur. Some cranksets may allow you to change just the chainrings for smaller ones.
Also, I have noted some entry level road bikes that have a very small small chainring, which would give lower gear ratios, all the other parts being the same, maybe you can fit one of those cranksets to your current bike.
A road crankset may not fit a mountain frame because the bigger chainrings may rub the chainstays, which in a mountain bike are more separated from each other to allow for the wider tires. A road crankset is designed for a narrower frame, so its chainrings and cranks are closer to frame's centerline. Conversely, an MTB crankset may put the chainrings too far from the frame's centreline for a road front derailleur to operate properly.
