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The idea is to use Ctrlr in a normal MULTI instance mode to design/test your panels, and do that in Standalone (normal executable not hosted).
This gives you the advantage of better window handling, better keyboard handling etc.
When hosting as a plugin, there are always issues with that stuff, and i don’t know of one single plugin (no matter how expensive) that covers all those issues in all hosts on all platforms.
I don’t have a budget/time i can spend on fixing all those quirks. But the exported instance of your panel should act like a normal plugin with parameters built in, that’s why this option was added.
So in short design/test standalone, run/use plugin.