Then you'll only end up with users that are willing to put up with that, and you will not get users that perceive this as a major inconvenience (I'm in this camp, and I suspect many, many others are too.)
I agree some platforms make multiple accounts hard to the point where you're registering multiple free email accounts, installing multiple browsers and using incognito mode, etc.
That is not inherently the case, and can be quite the opposite when allowing users to control multiple accounts is part of the software's design.
If you're forced to create one account per instance, there's no way to do something as simple as "merge comments from two instances into a single stream", which supposedly was the selling point of federated systems like Mastodon.
Obviously "topic" is the easiest way to differentiate instances today, but when was the last time you choose an email provider based on "topic" (or even domain name, for that matter)?
that said, you don't actually need multiple accounts to join conversations on other servers/topics. any account can talk to any other account on whatever server they happen to be registered on.
alts are more about identity than topics, in any case. in some cases, the topics you interact with are different, but that mostly depends on how much your want to differentiate your various identities.