Due to the way that fandom was at the time AO3 was being conceived and organized, pseudonyms do NOT hide your work from your main identity in any way. All pseuds of one account link back to the same account.

If you want an account to publish under that isn’t linked to your main, you just have to use another email account and create a separate one. It’s honestly not all that annoying, we have 2 just because of system reasons.