The Nomad Factory VST3s (80s Spaces, All-Tec EQs and Pulse-Tec EQs) have folders with a suffix of .vst3 and work fine, as does Suurge XT, so it's not something absolute about the .vst suffix on the folder calling the problem.
What are the contents of a "broken" .vst3 folder, as I guess it may be something inside the folder that is causing the issue.
That aside, I can see how a folder named equal to a file inside the folder could cause unexpected behaviour (recursion oddities). It also plain looks wrong!