After some playing around with this in a VM I think I've discovered that I can manually install the compiled game.libretro addon without issue in a custom build. So that's good.
I think my overall issue, and question, is whycan't I install the addon from the LibreELEC repository directly from within the custom build? When I browse the LibreELEC repo after a clean install of my custom build the Libretro Compatibility addon is hidden from view, guessing that it's deemed "incompatible". I'm thinking this is what initially broke it on my production media center as I installed it over a regular LibreELEC build and the addon was immediately disabled after reboot and I couldn't re-install from the repo at that point either. I had to compile and manually install. The versioning, as pointed out above, didn't have anything to do with it.
So I guess to summarize my question - is there something about a custom build that would filter out binary addons (Libretro specifically) when browsing the LibreELEC repository? Is this filter based on the OS version or something provided by Kodi? Ultimately if I can install from the main repo I'd prefer that to compiling addons.