You can just drop a patch into a folder, and every time you re/install or upgrade a package, it'll get applied!
You know that weird thing that bothers you in that specific software? That random popup when you start it? That additional, unneeded "ok" prompt? That donation-begging screen? That stupid checkmark checked on/off by default when it should be off/on instead?
Well, make a patch to fix it, drop it into /etc/portage/patches/// and it'll get applied automatically every time! And if it's truly a minor thing that bugs you, that patch will work for many new versions too!
(no, i'm not being paid by gentoo to promote them)