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I don't know why, but I was thinking that you were working towards a EasyOS Base (Kirkstone at present) plus individual containers for other versions such as void, deb, ubuntu, .... This may have got around the problems of changed and mixed linux's configurations as well as allow other versions to be tested in a standard build before individual release.
The problem with containers is they are not a very suitable environment to running other distributions. Too many limitations and compromises.
A Virtual Machine is much better to run another OS, and that is already taken care of with Qemu etc.
OK, so can it be done in some way to deal with the problem that arrises when mixing 'source package bases'?
I don't understand the question.
Containers inherit the kernel, Xorg, no systemd, no pipewire, no polkit, and more, of the host OS, and may be a very poor fit for other distros.
It is not worthwhile pursuing that direction.