So inverted switches still work with gmk they just feel different/wrong? Either way it would probably be best to change this if possible.
This is a touchy topic and some people have firm opinions. I firmly believe that upside down switches have issues with all cherry profile keycaps. (SA, DSA, OEM have no such issue)
I have many keyboards with upside down switches and can tell you that every GMK set and ePBT set I have (7 in total) does not bottom out properly on the QWERTY and home rows. The keycaps make contact with the switch before it bottoms out completely. It has nothing to do with LEDs, it is the switch housing that makes contact. The proper bottom of the switch falls off quickly. However, the proper top plateaus out for longer. When you turn that switch upside down, the keycap hits slightly.
It is much more noticeable with linear switches. They do work, yes. They will allow you to actuate the key. And if you are not too picky about switch evenness across the board it will not bother you much.
Some people will deny this is a thing. In my eyes, they are either numb in the fingers and hard of hearing, or there is some sort of cherry profile from before my sets were made that doesn't have the issue.