This is a good point about design choices when writing villains. Just remember to ask yourself “why do these characteristics make me think of them as villainous?”. There just needs to be balance.
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You can also play the villain TO those stereotypes, and have the heroes offended by the way the villain badly represents everyone else out there who possesses the same characteristic/s. This underscores that the stereotype is as much the villain in the equation as your BBEG.
I remember one D&D group where they had a villainous gay gnome necromancer of the darkest stripe as the B(irony)BEG of the campaign; and yet, no-one was offended by those facts. They were offended by the fact that the villain made all other gnomes in the area look like villains, that they made every necromancer in the district look like a depraved sociopath with a necrophilia shtick, and that they tried to corrupt other gay people into supporting their villainy out of a sense of gay solidarity. The villain made the heroes hate them not for being gay or a gnome or even a necromancer, but for making other gay people and gnomes and necromancers look bad to everyone else. And it worked brilliantly.
Sometimes, there’s a degree of bravery to utilizing a known villainous stereotype in your villain. It only becomes a problem when you fail to underscore that you ARE utilizing a stereotype, and that everyone outside of the villain’s immediate circle HATES the bad guy at least as much for the way they live up to the stereotype as for any of their other villainy. Because when you make that plain, you also villainize the misuse of the stereotype: the villain becomes offensive to everyone because they either don’t care about or actively encourage the demonization of all of the innocents who also manifest the stereotyped characteristic.