On a car with a normal metal roof, that has either builtin rails or typical screwholes for crossbar mounting exposed merely by lifting up little flaps, I wouldn't hesitate to use reputable aftermarket crossbars from a company like Yakima, if they seemed more to your liking than the OEM crossbar offering.
However with the unusual hidden screwhole arrangement + glass roof on these cars, and the stories I've seen of even Tesla OEM crossbars seemingly triggering roof glass fractures, and sometimes Tesla pushing back on covering that under warranty, I personally wouldn't risk using any aftermarket crossbars on this car, unless I was okay with potentially having to pay for a roof replacement out of pocket / insurance.
I'm actually scared enough that I've contemplated paying Tesla service to install my crossbars the first time I mount them up, so that if it turns out my car has serious fitment issues, it's clearly their fault and not mine. Before this car I would never have imagined paying anyone else just to mount crossbars on my own car!
The OE crossbar mounting for my Model S seems unnecessarily clunky compared to my past Subarus, but at least its mounting points are well separated from the roof glass. The Model 3's setup kind of bugs me to be honest.
This is just my 2c, not expert advice, and not based on actual experience with aftermarket crossbars on these cars.