Ok, I managed to find one mention of changes to the Gatekeeper mechanism in Sierra, one of which involves unsigned apps which includes MoI. There's some kind of virtual file relocation for unsigned apps run from /Applications and then my guess is that unsigned apps not run from /Applications are read only which won't work with MoI currently.

Seems like Apple is always changing something every year to make life difficult... Hopefully V4 will improve this situation a lot though since the MoI v4 Mac version will have a lot simpler structure to it than before.

- Michael