I agree with this, but I would also like to mention how it makes no sense that the great Bridge of Myrrdin is a Chapter in CF, when the Empire already occupys Garreg Mach. On the topic of maps, something I noticed in terms of maps is that each country has three major location: a field, a fortress, and the capital (Adrestia also gets the castle), though that's also me assuming that VW Chapter 22 is supposed to be Leister's field map, and one could argue Firihad has two maps.
I can appreciate all the analysis done in this post, but I would say that while of course the gameplay is very important, Three Houses' story was considered more important, based on all the reused maps, the simplistic cutscene backgrounds etc. While it does make sense for a secret route to be shorter, as others have mentioned, CF just doesn't have enough room to breath. Now, yes, the empire had the upper hand from the get go, going from the border of Liester straight to the Capital doesn't make much sense.
That said, you're right that fixing it isn't an easy task when it comes to balancing difficulty; just look how much fighting games have to adjust whenever they add one new fighter. Yes, we want a more... filled out? Story, but it's not an easy task.