The roof is made to accept a sunroof, whether you get the factory installed or not. There are no additional cross braces if you opt to not get the factory sunroof, so installing an aftermarket one is easy and should be OK.
The part number for the short overhead console, I think, is 15065809. Personally, I would keep your aftermarket sunroof and either get the factory short console installed or find one of the aftermarket consoles to install.
Here is a blow up of the stock sunroof with the part numbers.
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