Is it really gonna hurt anything.....probably not. Should work o.k.
Should it be that way.....no way. It should have been indexed correctly and the top ports should be at exactly the top.
Sounds like a smith that either doesn't have the skills he should, or else he just doesn't care.
If he won't fixt it, you can have a "good" smith index it properly by facing it off properly until the top ports are actually on top.
I had a local smith install a brake for me many years back and it too was not indexed properly. He thought it was o.k.
, he never touched another gun of mine.;);)