In the preferences, near the bottom (once you have the BioFormats plugin added), you can list the file extensions you want to include or exclude.
The stable release accesses the Extensions folder (or whatever you set as the extensions folder in the Preferences) to look for a copy of BioFormats. The milestone versions have one built in, but also doesn’t default to assigning any extensions folder at all. I am not sure you can change BioFormats in a milestone without rebuilding.
Attempting to force some of the milestones to use an extensions folder that contained a BioFormats plugin caused “bad things.” I’m not sure if this is still the case in m4.
I’m not really a programmer, just learned a little scripting, and pretty much only use QuPath in Windows. For many of these formats, QuPath will default to Openslide when BioFormats is prohibited. If Openslide is expected to work.