Yes, they’ll run into the same theme conflicts, but I believe discourse the company is going to treat themes as separate, and plugins as derivative. So you can’t develop a plugin that isn’t GPL, but you could make themes, as long as they don’t modify th operation of the forums underlying mechanism, ie a plugin.
There’s going to be a lot of back and forth about what is and isn’t under the GPL.
Still, there’s a case to be made that if the API is well documented, and no code was derived from discourse, then an independently developed, but inter-operating plugin could be distributed under a different license. The end user would be responsible for combining the two, and using them, and as long as they didn’t distribute the resulting combination, they’d still be in compliance with both the GPL discourse, and the proprietary licensed plugin. One could probably come up with a legally binding license for the plugin that would prevent further distribution, and thus tie the hands of the person that integrates it with their own copy of discourse.
It’s all very hand wavy, but certainly an interesting exercise in software licensing schemes.