Removing user from membershipgroupid=0 in the site level will remove users from the site level. The user still be present within SPO and can access other sites where he is not removed from. When you remove user from here, he is actual removed from user information list (which is present at each site level).
Check out this article: https://learn.microsoft.com/en-us/sharepoint/remove-users#remove-people-from-the-userinfo-list
this talks about how to properly remove user from SPO and then from each site level User Info List (they still have reference here).