Hi
Thank you for sharing the news. That is really helpful. I've made a note, and I have also filed a bug report about this too.
Ok, so the only solution I have that might work - is to set Motion to open to a new project - instead of the project browser.
If you go into your Motion preferences - and in general - set the start up action to 'create new project' - so this will go directly into Motion instead of activating the project browser. It is the project browser that searches for all of your plugins to preload - so if we skip the browser - maybe we can skip the pop-up.

..you need to then go the 'general' options - and choose the default motion template that you want to create.

I am not sure if this will work to stop the pop up - but you can try this and see.