I'd like to provide comments to all of your questions/responses, but I'm short on time so I'll do what I can now. Hopefully it will clear up some of it.
See
this link for a couple pictures of my soffit build. It's not too much farther along than it was in the picture.
OK, after looking at the pics, I see what you're talking about. In essence, it's a home brew storage shelf that you've got running around (most of) the perimeter of the space. It's that shelving which is framed with 2x4s, not the ceiling itself.
Not sure of code requirements, and I've never been through the NEC code in any detail. I have done HVAC work which required some electrical work/inspections. I also have an electronics background. I'm not an inspector though, and don't claim to know the many code requirements other than some of the obvious ones.
With that said, my house was inspected in 2006 when it was built. I verified that the ceiling mounted GDO outlets are on the same circuit as my living room outlets.
That's not ideal; but as you pointed out, it's fairly common. And as long as it is ONLY the GDO(s) which share that circuit with the Living Room, it's probably not a major practical problem.
In fact, every house I've lived in across several states has been that way, which were all built between '97 and 2006 (6 houses total/3 different states).
You move around a lot! Military, perhaps?
Me, I'm 27 years into my "Five-Year House".
That may be a new code requirement, which if I understand correctly, wouldn't have to be updated unless a change to that circuit was necessary (which it wouldn't be in this case).
I can't tell you which code cycle the "all GFCIs" requirement first appeared in; I suspect it was 2008; but I know for sure that it is part of the 2011 edition. As for whether or not you are "required" to observe it, that can depend on a couple of things, including the overall scope of the work (i.e., if the "remodel project" is major enough, you COULD be forced to update stuff that you otherwise would not be touching; all praise bureaucracy!

).
Next up, the single outlet that is in the garage is a GFCI. The load side of this outlet supplies the three additional outdoor outlets on the house (all have weatherproof covers). So the single garage outlet and the three outdoor outlets are GFCI protected.
Correct.
Additional outlets added to the garage would be added to the LOAD side of the GFCI in the garage, so they would be protected as well.
Well... Also correct,
IF one presumes that ALL of the outlets will be fed from a single circuit. However, that is NOT what I usually recommend, at least if your plans for the garage (and particularly the work you expect to do in it) are at all ambitious. I prefer at least two 20A circuits to feed the general-purpose 120V outlets, even in relatively modest residential garages (with "relatively modest" still being defined as "more than a glorified car-parking facility").
The framing confusion will likely be cleared up after seeing the shelving pictures in the link above. Maybe "soffit" is the wrong term, but it has been used for many similar installs on the forum, so I adopted the same term. The lights would be installed in the bottom of the shelving, shining down below the frame (which is built using 2x4 construction). It would basically shine down to where the tool box is located.
As such, they are effectively task lights. If you do NOT plan to install cabinetry or additional shelving above your workbench, that could work fine; and the wrap-type fixtures I cited earlier would still be appropriate. They would surface-mount to the underside of your platform/soffit/shelf, with the wiring running through the framing.
But that still leaves the general lighting for the space as a whole to be dealt with.
Since I have not done plug-in lights in the garage before, I have no experience with lights plugged into GFCI protected outlets. That is very good info to have. I'm not sure of the best option to power the lights if that is the case.
I'd hard-wire them, without question. Install one or more switches to control them, as appropriate.
It would me much more work to get the current light wiring over to the "soffit" cabinet lights.
Why so? You're surely going to need to get power over there in any event, and NOT just for the lights. Workbenches (and the areas immediately adjacent to them) tend to have a strong gravitational pull on all things electrical -- electric hand tools (drills, sanders, etc.), rechargers for your various cordless tools, the stereo system (or at least a decent radio), maybe a bench grinder or small drill press, perhaps even a countertop beer fridge... and so on. In short, I can't imagine a
useful workbench without a generous supply of electricity close at hand.
I also don't necessarily want all of the lights coming on with one switch (which is currently located in the living room adjacent to the garage).
That's easy enough to deal with. And I agree -- the switching needs to be much more granular and much more convenient than what you just described.
Well look at that, I had time after all

.
As the saying goes, you didn't have time to write a
short message. (I often don't, either.

)