Hmmm...part of that question seems to me something that should be addressed in terms of time line from the show; this is 1000 years after the end of mass effect but is it also exactly a 1000 years from the most recent episode of MLP? What kind of evolution has pony kind undergone in that time period? Perhaps Alicorns are far more common now to the point that they are a small 4th species. They wouldn't have princess powers, but would be about average in all 3 areas of pony abilities? Just a thought

As for an Alicorn's presence in this game it seems necessary given pony culture and history. Perhaps a recently minted princess is given the role of liason/representative. It would make sense to me that the greater forces of equestria would lead a pony to that destiney as it clearly did for cadence and twilight.

As for the magic...that, for me at least, comes back to what the MLP time line is. I could see 1000 years from present MLP with them being a space fairing race, that their understanding of magic has jumped leaps and bounds ( I'd even assume their space vessels work on a combination of magic and tech ) to the point where unique forms of magic have been developed for the earth and Pegasus ponies. But if this is recently after the latest episodes I'd say it would be unlikely such drastic magical advancements have happened.