GitHub also require MFA authentication since this year.
Does it mean that any MFA authentication now has same leaks?
Other than my banks, none of the systems I've enabled MFA for required a telephone number.
That includes: Dropbox, GitHub, Slack, Facebook, Nintendo, Google, Login.gov and the Digidentity.eu variant of Gov.uk Verify.
Everywhere it was possible I used my FIDO Security Keys which are phishing proof, impractical to de-anonymise and foolproof because the site has no secrets to leak. Whenever I hear that a site I already used MFA for gained WebAuthn or U2F I go back and switch that site to Security Keys.
Everywhere else I used TOTP (Google Authenticator) which can be phished using a live proxy and the site could leak their copy of your TOTP secret (not the changing code, but the secret that drives it) but other than those two concerns it's pretty safe. At least nobody can work out your real world identity by knowing your TOTP secrets.
The particularly nice thing about FIDO Security Keys that's relevant here is even a hideously incompetent implementation doesn't hurt you. The Relying Party (in this case Twitter) doesn't end up with any secrets, they get an apparently random "cookie" value to give back to you when they want you to prove you've still got that key, and a elliptic curve public key that doesn't correlate to anything except your login on their site. If they screwed up so badly that the Twitter web site showed a user's U2F parameters to every single visitor looking at their tweets it not only wouldn't unmask any pseudonyms used (as a phone number definitely would) it wouldn't even make it easier to login in as that user. FIDO is the right thing everywhere that a second factor is needed, but even more so when you don't trust the implementers to do a good job.
Also, if you try requesting for an API key, they insist that you add a phone number to your account.