So the reason why we don't save scores when the game is modded is due to the fact that a gameplay altering mod could make the game significantly easier to beat, and there'd be no way to tell if you've gotten a legit S rank or not.
For example, someone could make a weapon skin mod and then sneak in an AI mod that, let's say, makes them immediately surrender on sight and could easily win the game that way.
We still need to figure out a way to differentiate between different types of mods or detect gameplay altering mods, so that you can still use a weapon skin mod or any other non-gameplay altering mod.
We know this sucks but we haven't found a reliable solution yet, so this is on the backburner for now.
Also, we want to keep the official vanilla scores too, just so there isn't any confusion if you achieved that score with a gameplay altering mod or not. But the idea of recording unofficial scores would be neat as well, that can be implemented.