I'm sorry but they likely won't ever go back and change old houses like this.There have been a lot of requests over the years, for example to remove the invisible wall at the roof of Twin Arches, but they won't do it. The last time I remember them changing invisible walls, it was for the worse (lol), in Daggerfall Overlook and Earthtear Caverns...
If you want a small rectangular house with upper space potential, try Autumn's GateI know it's not what you wanted, but maybe you can create your second-floor idea somewhere else (most other small houses have non-blocked-off space for a second floor).
Edit: Actually, found this forum thread and there is more info and detail about the upper storey space available in several houses! I'm sure it will be more useful to see examples! https://forums.elderscrollsonline.com/en/discussion/380571/houses-you-can-build-up-in-without-hitting-invisible-walls-barriers