I had my worries with the stock and height of the eotech, but it's perfect, cowitnesses well with the irons too. I have no plans to change the current stock.
For the mags, they came with IMI mags, I haven't tried em out yet but I can speculate it's probably pinned to 5rds. I'd say magpul mags will probably work with this gun. As for if it's better then an Swiss Arms rifle, I have never handled one so I can't really say.