Xojo keeps a cache folder for each version Xojo version, so you may have something like in the picture on the right in your ~/Library/Caches/Xojo folder.
As you see, we just dropped in two plugins for the screenshot, but we did use console, desktop, iOS and web targets in two different versions. Xojo creates object files for the linker to use those plugins in the compilation process. If that works well, you only get a pre-compilation dialog every few weeks, when you may install a new plugin version.
Now if you have more than one copy of the same Xojo version on macOS, they share a cache folder. If one Xojo version belongs to a project with a few plugins and the other version has not the same plugins, the Xojo IDE will notice that the cache doesn't match the plugins folder and rebuild the cache each time you switch.
It is perfectly fine to have one plugins folder per version with different content. But if you switch one version between two plugins folder, then you see pre-compilation every time.