May be you consider to alter the process of tunnel down building:
1) rail subway (which is obviously much bigger construction) placeable just by click (and removable, what a very convenient), but character tunnel need to be drilled and cannot be removed.
2) may be you should make both entities placeable with drill (more close to reality) or both hand-placeable (more convenient)

Also, if you make character tunnel hand-placeable it will technically fix quality issue 😁

I'm still not sure about the best compromise.
Making the entrances placeable by hand seems too easy to gain the opportunity for switching surfaces. Maybe if I set the initial research cost much higher.
Requiring the subway to be drilled makes rebuilding your setup too difficult which wouldn't be fun anymore.
The entrance is not part of a factory/logistics setup, so not much reasons for a rebuild.

I'm still not sure about the best compromise.
Making the entrances placeable by hand seems too easy to gain the opportunity for switching surfaces. Maybe if I set the initial research cost much higher.

If we take for example Factorissimo mod, which technically close to yours (access to other surfaces), they using very high research prices. As i remember starts from 1k bottles.

Requiring the subway to be drilled makes rebuilding your setup too difficult which wouldn't be fun anymore.

Yeah, I talking exactly about that. Overcomplicated placing steals fun from game, but what about to use other ways to omit oversimplifying? For example force player to use vents or lights underground? Also we could make entraces to removable not by hand, but with some other expensive one-use tool. I think easy but expensive is better then hard but cheap.

The entrance is not part of a factory/logistics setup, so not much reasons for a rebuild.

Hmm, obviously to build factory/logistics setup you have to get into entrance :)
And for some reasons if you built it in wrong place, you will have to build another one, instead of just remove old one.
As for me, underground ifrastructure is closely interlived with onground one, so if i rebulid upper base in some cases, i will change the entrance, related to current conveniences.
Then, i might change my mind i decide to completely remove character-entrance, for example, in multiplayer, may be i want to make hidden from others underground base :)

And i just thought about additional interesting thing - what about possibility to build passway from down level to upper? Now there is no such option.

Yeah, I talking exactly about that. Overcomplicated placing steals fun from game, but what about to use other ways to omit oversimplifying? For example force player to use vents or lights underground? Also we could make entraces to removable not by hand, but with some other expensive one-use tool. I think easy but expensive is better then hard but cheap.

It is already possible to seal entrances using cave sealing (filling up with stone).

And i just thought about additional interesting thing - what about possibility to build passway from down level to upper? Now there is no such option.

This would require futher concept creation and also graphical stuff. This also leads to the possibility of "bypassing"/avoiding enemy bases and other stuff

It is already possible to seal entrances using cave sealing (filling up with stone).

Alright, thanks!

This would require futher concept creation and also graphical stuff.

Why just not to use same graphics as entrance. For now, at least.

This also leads to the possibility of "bypassing"/avoiding enemy bases and other stuff

Very good and useful feature. For example on maps with hard and powerful biters - to go under, build factory beneath, collect the power and bring revenge :)
Also there option make entrance attackable by biters, but when they step in one squre close to entrance - teleport them to underground surface near exit. That feature will make caves factories be attackable.

Why just not to use same graphics as entrance. For now, at least.

I meant the drill graphics. Having a normal mining drill but drilling upwards is ugly.

Very good and useful feature. For example on maps with hard and powerful biters - to go under, build factory beneath, collect the power and bring revenge :)
Also there option make entrance attackable by biters, but when they step in one squre close to entrance - teleport them to underground surface near exit. That feature will make caves factories be attackable.

Good point. A similar idea I had before is to "attract" enemies when you dig in a certain radius below them (currently, enemies have a chance to spawn underground only when creating new bases and if the underground is exposed on this position) - also see the mod https://mods.factorio.com/mod/WormAttack. Some of them will burrow down and hunt you, the other just "wait" for you if you dig a hole to the surface.
If playing in challenge mode, it shouldnt be ever possible to avoid enemies to get to far POIs.