This is not allowed for SEPA account, impossible to add a new account by default

Then I don't know what you want me to do about this. Stripe itself doesn't allow it.

For instance if a customer initiate an offline payment, clicks on the payment slip and come back after to pay by SEPA or credit card it's impossible. That just triggers a new basket => a new invoice for him and our backend

That's because the basket is then Pending. We do not have re-usable pending baskets. The reason is the pending state is meant to indicate a payment is on the way. If the basket is reused then what happens when the "on the way" payment arrives AND the new payment just made? We'll need to completely redo the basket pending state handling. I've added a feature ticket to look into this.

forge.joomlapolis.com/issues/8839

There's a lot to consider for this one as we don't want it causing some strange conflict with on-the-way payments and the follow up payment. Basically we don't want people being billed twice if their recurring payment method is pending.