Toilet Flange

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Didn't he tile under the toilet? He should have; that is standard practice. If not, have him come back and do that, or do it yourself. You must have tile under the toilet for the very reason you cite, plus if you ever change it in the future, the new toilet may have a different footprint.
I get the feeling that he didn't even put the toilet back in place, which he should have done. Then it would be his responsibility to make it work.
The flange should be level with the finish floor, but if it is just a little higher, it may still work ok. Set it in place to see.
At one daughter's place the contractor had the plumbers set the toilet flanges high in anticipation of using ceramic tile, which wasn't used. When I replaced the toilets recently, I found that the plumber had set one of them on several pennys to raise it up enough to work. And it did. For a more elegant solution, you can get plastic toilet wedges at a home center. Last choice in my book would be to mess with the flange.