I spent some time staring at the changes you made, and I admit I really cannot follow why it broke what I was doing, but it did.
This no longer works to access submodules/subfolders from git. Only the very first submodule is installed. Prior to 3.3.0a17 it worked. (I am not positive the last version it worked on.) Using a separate git clone works fine.
lib_extra_dirs = .piolibdeps/EnviroDIYLibs
Using "lib_extra_dirs = ." (or "lib_dir = .") causes all libraries in the global, lib, or .piolibdeps folders to be missed. This can be solved by adding "lib_ignore = .piolibdeps, .pioenvs" to the environment.
The dependencies are installed correctly from a library.json in a VCS URL.