Are you sure that it can't be crossed? That is new to me. Aren't there any other warnings which could cause this?
(I.e. about minimum sdk version or missing 64bit code)
And yes, It was (probably still is) possible to publish godots apks. Although the last time I tried, was some months ago though. (I also got that warning at that time.)
About Android Studio:
I didn't try to build with Android Studio, yet. Probably the game engine doesn't need to be recompiled. I'd try to create a minimal project and then extract the project files from the own apk and add them at the "right places".