I think there were historically interoperability issues, and there used to be (my version of mbin is quite old), and maybe still are issues federating dislikes (which stems from the way they were seen in kbin, which straddles both thread based and mastadonesque sides of the fediverse). But overall there's aren't the larger federation issues there used to be.
Right now, the choice mainly comes down to the interface you prefer, and if you perhaps want a limited ability to work with mastadon type posts. Since you can follow mastadon users and see their posts within the mbin interface.