Reddit admin has been pretty consistent about letting mods run the subs the way they want, except in cases where the mods are encouraging brigading or breaking laws. For the former, they’ll let that go a few years before they do anything about it, though.
Putting aside your specific situation: Threatening a site-wide ban for circumventing a sub’s ban comes from dealing with users that are complete pieces of shit and refuse to follow the sub rules and keep coming back with new accounts to troll. The site has to raise the stakes to get them to stop; what other options are there? I’ve been active on online forums for years; one had to ban a whole city for a while because users there kept logging in and starting shit (they were coordinating with each other).
On the other hand, if the user started another account and followed the sub’s rules, who would even think to check? It’s unlikely that person would get a sitewide ban.