There are some pretty big games built in unity, the money on the table is coming from them, (assuming reasonable licensing terms) not the small indie games.

I may be entirely off the mark, as I don't work in that part of the industry. But I've messed around with unity and it's not particularly unique compared to any other engine it competes with in my experience, particularly when it comes to actual runtime. Assets will need conversion and sure, the API shim will probably give a performance hit, but there's no reason I can see that unity is fundamentally different.