Say I create 3 accounts with my metamask (same seed phrase), if one account is "compromised" by a website, will it also affect the 2 other accounts if I didn't give the website any permission for the other 2?
Metamask accounts are not compromised by giving permission to a website. The permission only allows the website to see your public address, not your private key or seed phrase.
Typically, your account will be compromised if your seed phrase is stolen or lost. In that case, all the Metamask accounts that you generated with that seed phrase will be compromised.