I think the "Surfaces" GUI is not needed at all, the right one does the same thing

(this is only in Isolation None)

Good catch, I actually had another issue here that I noticed from your screenshot. Nauvis should be visible, but it was accidentally hidden. But, you're talking about a special case where the only other place you could view is Nauvis - and in that way there's no need to show the Surfaces - and in that case the Surfaces is set to hidden just to simplify the area.

For other cases, like when playing Space Age, the Surfaces remain; I know you said "awkward" positioning, but there's nearly nothing I can do about that, since that's how Wube has decided the layout should work. The only other options are along the top, which would be ridiculous because of the side, or completely free-floating and up to you to place.

Can you add a separate setting to force Surfaces to be hidden? I tried the NiceFill mod at one point and it created this absolutely blank surface which is now visible and won't make the Surface GUI go away. I'd assume same will go for mods like Factorissimo or any other ones that create them.

Or maybe you could add this one NiceFill surface to the list of surfaces that won't make the Surface GUI to show up. Any method would do.

Oh and also that Surface menu now also shows outside of the BPS, in my game's remote view.

All of that is intentional. If you hide that NiceFill surface, then this mod will react appropriately and no longer consider it one of the visible surfaces, but determining if it should be hidden is not a responsibility of this mod. The Surfaces list is a core feature of Factorio, and this aims to integrate with that; in the same way that you can access/build on other Planets, you can do the same with Sandboxes. I will consider a setting that forces it off while inside of Sandboxes, but honestly that's quite a specific request so I'm not sure.

If you hide that NiceFill surface

Wait, I can hide it manually for myself somehow? I didn't know that, how would I do that?

Okay, i deleted the NiceFill surface via console and i finally don't have the Surface GUI in BPS, but in Remote View (from the game) i still do (despite having only two surfaces that shouldn't trigger it)

The surfaces are also visible when you have mods like mech armor or stack inserter enabled. When I removed them and switched to Full Isolation the surface gui is no longer visible

I only have this thing on (https://mods.factorio.com/mod/enable-all-feature-flags) but SA is off and no additional mech armor/stack inserter mods. Still seeing the GUI 😔

Hmm, I enabled the feature flag mod and no suface gui on the map. weird.
Edit: And now I enabled the mech armor and ... no surface gui on the map. I'm out of ideas

I even tried to completely remove the mod, make a new save without it and install it again to maybe "reset" the surface GUI but even when i remove BPS i still get these ghost surfaces which i can't access but despite that are still there.