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Sure you can compile and install software the way you like. However, Gentoo has something called portage to handle installation, upgrading, configuring and deinstalling software in a much convenient yet still flexible way.
It should work correctly. If I understand this correctly you should list the corresponding Gentoo/Sabayone package in the package.provided file. This is used by portage for dependencies etc, i.e. it will only make a difference when you install other things with Portage that have some sort of relationship to those separately installed packages. I think I saw something somewhere that this is like saying to portage: "presume these packages are installed already".
I have never been in this situation myself, but this is how I understand it...
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