The present perfect "have become" is used to showed actions that are still in effect, or whose consequences are still in effect. We often use this for things that are experiential: "I have read that book" implies not only that I read it, but that the knowledge is still with me. So, we can only use present perfect when the subject is still in existence to experience those results.

"I have become a good GMAT test-taker" -> I'm still around, experiencing those results.

"Species have become extinct" -> If the species went extinct, they're not still around to experience those results. It makes more sense (and is more succinct) to say "species went extinct" or "species are extinct."

The other problem with B is that saying "most are disappearing before homo sapiens evolved" implies that they're still in the process of disappearing. The present progressive "are disappearing" is used for actions that are currently ongoing. In this sentence, the "disappearing" should happen long in the past.

A-have existed on our planet are already extinct, with most
Correct.

B-have existed on our planet have already become extinct and most are
Discussed above

C-existed on our planet have already become extinct, most of which have
The "have become" is not correct, as previously mentioned. "Most of which have disappearing" is not a correct structure.

D-exist on our planet have already become extinct, most
"Exist" is in the present tense - we need the existence/extinction to be in the past.

E- exist on our planet are now extinct, with most
Same issue as D.

Differences in verb tenses almost always reflect differences in meaning. For more on verb tense issues, see:
https://www.beatthegmat.com/make-tenses- ... tml#710451
https://www.beatthegmat.com/og-10-native ... tml#577377
https://www.beatthegmat.com/the-editor-o ... tml#710456

If you're interested, we have a free video on PERFECT TENSES (past, present and future): https://www.gmatprepnow.com/module/gmat- ... on?id=1178

Cheers,
Brent