There was at one time a YAF implementation in mojoPortal. This was done by someone in the community but it was a long time ago so I don't think it would work now.
As far as mojoPortal being developed to be compatible with "known" forum scripts, that would be extremely difficult because the mojoPortal Dev Team would have to constantly monitor numerous third-party scripts to make sure that mP is still compatible.
So, if you need to use a different forum script with mojoPortal, you could integrate it yourself and then share your findings with the community. mojoPortal is extremely flexible so integration of other .NET scripts is possible, the person doing the integration just needs to be good at .NET and know both mojoPortal and the "other" script very well.