Agreed, this decision seemed par for the course for an upstream project, most wouldn't want to accept distro-specific patches.
I agree as well. No distro-specific patches seems like a very reasonable position. Section 3.3 of the Debian New Maintainer's Guide explicitly recommends this approach to Debian package maintainers. In the interest of being good members of the open-source ecosystem I'm sure most other distros have a similar policy.
Now you have a series of patches.
Upstream bug fix: debian/patches/fix-gentoo-target.patch
Debian specific packaging modification: debian/patches/install.patch
Whenever you make changes that are not specific to the Debian package such as debian/patches/fix-gentoo-target.patch, be sure to send them to the upstream maintainer so they can be included in the next version of the program and be useful to everyone else. Also remember to avoid making your fixes specific to Debian or Linux - or even Unix! Make them portable. This will make your fixes much easier to apply.