I don't understand that. Why shouldn't it be possible to have two or
more tpm files put ordinary files into the same directory in a TEXMF
tree, and remove only their "own" files when they are removed? Maybe
I'm missing something specific to TeXLive, but generally I would say
that this is exactly the point of "packaging". At least if this is more
than just zip'ing up things, and keeps a list of installed files around
or in the installation program.
So we are at the same point for TL and other distribution,
Linux distributions surely do *not* have that problem; we can just move
supp-*.tex to a different deb/rpm than the other context files.