If a player joins a team then goes into gamemode 1, then logs out, they are put back into gamemode 0 when they return.

Is this an issue, or intended behaviour ?

Intended behavior. On login, the plugin needs to ensure that players are put into the appropriate gamemode for their role. Players changing gamemodes is not prevented in non-auto-mode, but it is undefined behavior. If a player needs to go back to gamemode 1, they will need to be changed everytime they relog. Until such behavior is defined properly (perhaps never), this is a wontfix.