Essentially I am wondering if wheelsets are manufactured differently for the front than the back wheels. I assume only the hubs and spoke holes?
Yes - they're totally different for a number of reasons.
The rear hub has a cassette on the right side, so the wheel has to be assembled dished. So the right side spokes are slightly shorter than the left-side spokes.
Right image shows something that MTBs have tried - having the right chainstay further from the bike's centerline than the left chainstay. This is not common on road bikes.
Rim profile can vary too. A front wheel can be flipped and used the other way around, (with the possible exception of directional tread on a tyre, and disk brakes.) So front wheels are built symmetrical. Rear wheels are dished, and as a side effect the nipples can be at different angles as they leave the rim.
Here's a cross-section of a MTB wheel that shows it nicely. The tyre is centered in its track about 2-4 millimetres to one side of where the spokes would be centered. You can see the hole where the spokes go through, and its part-way out of the valley. This is ONLY practical on the rear wheel and lets the builder use slightly more even spokes but still have effectively a "dished wheel"
In addition, the power of drive comes through the cassette, so the rear wheel might be laced with a variety of patterns. Most common is 3-cross, where each spoke crosses with three other spokes on its way to the rim. 2-cross would be slightly shorter spokes. Combinations like radial lacing on the non drive side and 2 or 3 cross are not as rare as they used to be.
Front wheel lacing seems to be favouring radial spoke design for simplicity, but that's at odds with front wheel disk brakes. So rim-brake road bikes will move to fewer spokes radially, but disk brake road bikes will drive it back to 3-cross and add spokes.
Spoke count matters too - the front wheel carries less load, so can "cope" with fewer spokes. The downside is a weaker wheel, which translates to a heavier rim.
Spokes might be bladed on the front and plain old round ones on the back. The front wheel runs in cleaner air, with more predictable aerodynamic effects. The rear wheel is in much choppier air, so bladed spokes have less beneficial effect.
So yes the front and rear can be assembled differently. The method to assemble them would be pretty much the same, as long as the wheelbuilder gets the crossing correct while adding spokes. Bladed spokes provide extra challenges, but nothing a wheelbuilder can't handle.