I reckon it’d depend significantly on the instance. Beehaw has a signup form reviewed by humans - measures like this are by no means perfect, but coupled with other bot detection software could help. If an instance developed a real issue with bots, other more strict instances could potentially ban up votes and comments from accounts on it.
At the very least, tracking instances that account interaction came from should be quite doable, so users part of more strict instances could filter out upvotes and comments from less strict instances if desired.
Yeah, I do agree Beehaw won’t be able to grow significantly if they keep doing things the way they’re doing them right now. At present point, they’re going to likely remain a more niche community long-term with how they’re operating. Who knows though, maybe this is what they want. Lemmy would have to do something different though without a herculean moderation effort.