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The bottom bracket height on some bikes can be adjusted 7.0mm by flipping a "chip" in the shock mount linkage. This also affects head tube angle by 0.5 degrees.
Theoretically speaking, What are the advantages and disadvantages of having a lower bottom bracket setting vs a higher setting?
in my experience. BB height affects stability of your ride, but mostly while standing on the pedals since you weight is then directly on the BB. but raising it 7mm may or may not make a difference in your ride. however, raising it ABOVE the axle height will make a dramatic difference in stability. BMX bikes are incredibly nimble (aka unstable) due to them having a BB higher than their axles, where as 29'ers will feel solid as a rock since they have a dropped BB height relative to their axles. it has to do with torque applied while standing. (i know wheel size also plays a factor but we're assuming spherical cow here). so considering that the DROP or RISE from the axle height affects the ride more than height, a 13in BB height on a BMX will feel much different than a 13 in BB height on a 29'er.
my track bike has a BB height equal to its axles, and its nimble and fun to ride, where as my road bike has a BB drop height relative to the axles and feels like a cruiser in comparison (both on 700c rims).
TL;DR higher BB, in relation to axle height, means a more nimble bike, lower BB is a more stable bike. especially while standing.
First, to answer the question - Bikes with lower bottom brackets are more stable (and less nimble), and bikes with higher bottom brackets are less stable (and more nimble). Lower bottom bracket height can also cause pedal clearance issues, although this can be accommodated with changes to riding style. In the case of a flip-chip, the slightly lower BB height in the low position comes along with a slacker head angle (which also contributes to high speed stability), and a slackened seat angle (which could be good or bad, depending on one's bio-mechanics and preferences).
In my experience, the lower position tends to favor high speed riding, while the higher position will be better for slower, more precise riding.
Spherical cow reference aside, the accepted answer falls victim to a common misconception - it is not the bottom bracket drop which matters to riders, it is the overall bottom bracket height from the ground. Only the latter is affected by wheel and tyre choices.
There is nothing magical about the bottom bracket height relative to the axle height - a bike does not 'hang' from the axles, rather it balances upon the tires. The bottom bracket height of a frame is often specified as BB drop because that metric is fixed, while the the actual height of the bottom bracket above the ground varies with the tire size.
Larger wheels correspond with increased stability not because the BB ends up lower relative to the axle, but due to the increased gyroscopic forces of the wheels, and the (typically) longer wheelbase necessary to accommodate the larger wheels.
Example - the difference in the radius of a 27.5 and 29 wheel diameter is 19mm (though the total varies with tire selection). If BB height relative to axle height determined the stability, a designer wanting to keep similar handling characteristics between a 27.5 and a 29 bikes would perhaps design in a couple mm less BB drop on the 29 (to account for the different characteristics of the larger wheels), which would result in a nearly 19mm higher absolute BB height on the 29r. If absolute BB height matters, then the designer might subtract a few mm from the absolute height on the 29r (again, to account for the different characteristics of the larger wheels), which would result in an increase in the BB drop of nearly 19mm.
Look at what they do in practice:
| BB height (mm)| BB drop (mm)
Santa Cruz Highball (27.5)| 314 | 40
Santa Cruz Highball (29) | 314 | 56
Devinci Troy 27.5 | 344 or 350 | 12 or 6* (flip chip in low or high)
Devinci Troy 29 | 339.5 or 346 | 31 or 25*
*bb drops were not given on the Devinci site, so I calculated these assuming a 712 mm diameter for 27.5, and a 742 diameter for 29.
BB height barely changes between equivalent 27.5 and 29 designs, while BB drop changes a lot. BB drop matters to builders, BB height matters to riders.
(Source: I know this because I design bikes.)
The bike may ride differently. The only way to find out whether it does anything for you is to buy the bike and try it. Ideally by running the same course repeatedly and writing down how you think the bike performs (and the lap times), while someone takes the bike off you, hands it to a mechanic who never sees you, and the mechanic swaps or doesn't swap the part in question. That way you have a double blind test.
One well-known framebuilder in the USA (whose name escapes me) did a very limited set of experiments with small variations in frame geometry in the 1990's, and concluded that no rider could tell the difference from less than half a degree change in headset angle. Unfortunately those experiments were fairly expensive to conduct because he had to make 3 or 4 "identical" bikes and find a set of riders who were all the same size. Basically he let the normal variation in a hand-built bike create the variations, and measured the bike after they were built to find out what he had. Then the riders rode the bikes and rated them against each other. The conclusion was that a millimetre variation in tube lengths and half a degree in angles did not cause any repeatable difference in rider evaluation. But with sample sizes of 3 frames and five riders it's not statistically significant.
I suspect Trek has similar research (as a result of employing Mike Burrows if nothing else) and would not be at all surprised to find that all major manufacturers have done similar things and specify the tolerances in their manufacturing accordingly.
