Dropbox, Facebook, Google, GitHub, GitLab, even Login.gov works fine with multiple tokens.
More sites should do WebAuthn (you should not do greenfield deployments of U2F today, WebAuthn is the standard). Yes, AWS should fix their feature but that shouldn't block the next ten would-be Unicorns from doing WebAuthn.
But none of these support U2F or WebAuthn at all. The problem isn't that they need to support "multiple" tokens except in the sense that they don't support any at all.
It doesn't make sense to try to "support multiple keys" for TOTP. You can copy-paste TOTP seeds if that's what you want and feel comfortable with, if the site tries to allow you to use any of N seeds they not only increase their system complexity they also reduce their security by a factor of N which makes no sense.
Edited to add: OK, Coinbase does now have U2F and they clearly state you can use "a maximum of 5 keys" which feels like that's enough.
Dropbox, Facebook, Google, GitHub, GitLab, even Login.gov works fine with multiple tokens.
More sites should do WebAuthn (you should not do greenfield deployments of U2F today, WebAuthn is the standard). Yes, AWS should fix their feature but that shouldn't block the next ten would-be Unicorns from doing WebAuthn.