If its set already ( rapid set ) , I'd leave it until finished ( grouted ) and see how it works . If it doesn't drain right the only extra job is removing the grout , if its ok , then it's just a case of whether or not can live with it . Dont forget once the grouts in it should blend a little better and you might not notice so much.
I'm not making excuses for anyone here , just saying it's not the end of the world . All said and done though you are the paying customer so it's entirely up to you.
For me it doesn't look terrible , odd maybe , but not terrible.
Just as a side issue ( and this nothing against the OP ) I dont understand why more people don't go for a matching mosaic in the former , looks miles better than all the envelope cutting imho , aesthetically , just my view though.
Diggy