Ah! Scaling and consistency is almost an endless topic. So...
Switch off your brain. Making sense out of FFVII's physically impossible BGs is a waste of time. The stairwell in upper Shinra Building, for example, is impossible. The way the stairwell goes up would cause the each subsequent floor to have an overbite. I know because I tried to model it as a continuous model for the Mako Dawn mod. You don't notice because you never compare the BGs side by side. No one besides developers will notice — you're just hyper concious of it because you're making it.
Unless you're planning on solving all continuity issues, my suggestion would be not to worry about it and focus on making it look nice, not logical. Unfortunately, that'll occasionally mean recreating tweaking / things even when they're supposed to be part of the same object.
I don't think that making sense of the backgrounds is a waste of time. I agree that making a perfect matching of all the connected scenes with extremely realistic proportions is not possible, however. Nevertheless, I do believe in the importance of ensuring consistency in these environments, because having characters in a believable surrounding helps having the player immersed in the world (suspension of disbelief, if you would call it). With that in mind, I'll always do my best to make the environments look logical, or at least "as logical as they can possibly be".
Now, with these criteria, there will always be some compromise to be made (as you mentioned by "tweaking things"), and I have already made a few. For instance, the houses of the outdoor scene of the Sector 5 slums are coarsely undersized (particularly when compared to the indoor counterparts of the shops). Hence, when trying to do the outside/inside matching, it can't work perfectly on a 1:1 scale. The compromise I made in that occasion was to just cut out pieces of the shop that wouldn't fit in the outside scene (it visually works because, from the outside, you only see a small fraction of the indoor environment). For the bus scene, there are some details I am going to change (namely, the driver's seat location). And there will be some other design changes along the way. I also believe it makes sense to take some liberties from the original design, since scaling everything up on the same proportions as the original would create a bunch of absurdly sized objects (mostly smaller objects, like a tin can, a soda bottle, a tea cup, the steps of a staircase, etc).
All in all, I think it is worth to put a lot of thought into scaling, redesigning, and what I would call "reconciliation of discrepancies between environments".
One other thing: thanks to Kaldarasha, I am now aware of what can be done about the character sizes using Makou Reactor, and that will be a huge help for solving most scale inconsistencies.
Do we have the ability to make/modify walkmeshes? That's obviously taking greater liberties with the game than this project was ever meant to, but it's pretty much necessary if you want the world to actually fit together properly.
Makou Reactor has some possibilities to edit the walkmesh, but it seems to be a bit buggy and uncomfortable. But the option is there...
Given the extremely remote possibilities of walkmesh modifications, I have based all my designs on the constraint that the walkmesh cannot be changed. I will keep on working that way until the day someone ends up with a bug-free in-game test. Even if the walkmesh can be altered and help to solve consistency issues, I would rather go for small edits, not something that would drastically change the whole scene (or at least, not in the near future). That being said, I'll try to keep an eye on the progress made in that department (or, if the person willing to test walkmesh alteration would keep me informed, it would be greatly appreciated

).