Not a good idea, in general it would be nicer to use the shared copy of zlib already present in the system, to avoid having to load more data (zlib is almost always already present in memory) and to allow fixes in zlib to be shared by its users too.
I deleted zlib.h and zconf.h, which are the only files in erts/emulator/zlib/ that belong to the Gentoo zlib package. The other files cannot be linked to a package by me, so I don't know, if I can substitute them. lookout for -r1
Duh, where those two files are (${S}/erts/emulator/zlib) are contained, the rest of the files are not present in zlib package because they are *built* by the zlib package into libz.so. You should remove the whole source directory and link against the installed libz.so.
After struggling with upstream, we cleared out, that erlang cannot use system's zlib due to heavy patching. As the current stable includes a vulnerable zlib I already filed a security bug for the newest....maybe upstream will do something about it for R12.