Using --enable-system-site-packages is broken:

• first, the version of sage_conf inside the venv is installed in such a crooked way that it will not override the one installed in the system site-packages, in spite the sage venv site-packages being listed before the system site-packages in sys.path.
• the version of sage_conf.py I have in my system doesn't define GAP_ROOT_PATHS (not a thing in 10.2). This results in an incredibly scary-looking error (to simulate try GAP_ROOT_PATHS=/ sage -c 'gap(1)' or worse GAP_ROOT_PATHS=/ sage -c 'libgap(1)').
• I don't know how to fix the search order for sage_conf so I just added GAP_ROOT_PATHS to the system sage_conf (I can't remove it since I don't want to break sage for other users)
• With that fixed, almost all tests pass except some in src/sage_docbuild and the top comment in src/sage/env.py

Originally posted by @tornaria in #36181 (comment)

EDIT: some relevant notes that are mentioned in the original post:

• I'm testing with PR Python 3.12.x #36181 at 29130ea, since my system python is 3.12
• I used ./configure --enable-system-site-packages --disable-doc