Oh, OK so when fuse not shorting everything sounds like working as expected - I didn't realize you were able to control headlamps in daytime - cool
I kind of forgot what the rear lamp assembly on Malibu looks in regards to how the bulbs and socket work so maybe there is not an issue if you leave a bulb out in regards to sealing. I now seem to remember there is a seal around the whole assembly with bulbs that snaps into the lamp so removing a bulb probably no big deal. However the wire I suggested you remove will cause a leak path into the lamp assembly so this is only a short term test. If that resolves the problem I am sure you could find something to plug the open cavity - however we haven't been having the greatest luck yet so we'll see what happens.
It might be that there was poor retention of bulb in the socket leading to high resistance and heat build-up which caused the damage you are seeing. I know that I have seen an awful lot of this body style that don't have all 4 stop lamps working. Don't know how this could be causing the intermittent tail lamp short but I know there is a network of "metal frets" in this assembly and maybe one somehow is now shorting out against a ground due to this other damage.