All your 2FA apps, token, security keys, certificates and what not only protect the authentication (and in the case of online banking, a few other actions like transferring money). After that, a single bearer token authenticates each request. If your endpoint is compromised, the attackers will simply steal the bearer token after you authenticate.
That's true, but in terms of system design you definitely should ask to see the proof of identity again during unusual transactions and not just that bearer token - for example attempts to add or remove 2FA should need that extra step, as well as say high value financial transactions or irreversible system changes.