When using insync-headless and configuring a new account for the first time, Insync currently has a default action of automatically starting to sync everything in My Drive. If however you plan to only sync selective folders, you then have to go and deselect everything manually, leave Insync to finish its initial scan (which can take hours or days depending on how big your Drive storage is), and only then go back and select the correct folders to sync.
It usually takes me 2 days on average when I set up a new configuration of Insync just to get to the point where the correct folders have been selected and syncing can actually start.
It would be a much better idea to have a command line option with add_account that will tell Insync not to do an automatic full sync immediately after adding the account. If you then provide that parameter, Insync will add the account and retrieve the full folder set but not do anything else. This will then enable you to go into selective sync and select the relevant folders before its starts its initial sync, and in the process save you a lot of time.
If on the other hand you don't specifically provide the parameter, then Insync will just take its default action of starting a full sync after adding.