Paying the basket from backend is how Offline gateway functions. It should be firing the CBSubs triggers fire. It's not going to fire onAfterUserStore unless it needs to, which in most cases is never as CBSubs has its own triggers and rarely alters the users data except in cases of Usergroups, block state, or CBSubs Fields.

onAfterUserStore doesn't exist. I'm not sure where you're getting that trigger from. It's onAfterUserUpdate (frontend) and onAfterUpdateUser (backend). Both of which CBSubs will fire if the user object is modified. CB user store always calls Joomla user store first, which would cause Joomla to fire its events as necessary. The Joomla event is onUserAfterSave, which is handled by Joomla when the CMS user store is triggered. Direct database changes won't have any affect though as they're not storing the user object.

Well it does not seem to fire integrations to acymailing lists for instance. (users are recorded on lists but not activated)

If they're added to the list then the integration is working. Them not activating could be a configuration issue. You need to ensure you've selected newsletters to add instead of remove.

You could try using CB Auto Actions with the below trigger usages.

Plan Active
Triggers: onCPayUserStateChange
User: Automatic
Access: Everybody
Conditional 1: [var3] Equal To PLAN_ID_HERE
Conditional 2: [var2] Equal To A

Plan Expired
Triggers: onCPayUserStateChange
User: Automatic
Access: Everybody
Conditional 1: [var3] Equal To PLAN_ID_HERE
Conditional 2: [var2] Equal To X