There’s no downside. It allows changing stripe accounts and moving subscription to another stripe account as well as manually adding users which sometimes is a must. As written above I don’t know what the additional check is meant for. It doesn’t exist for PayPal either.
Happy to have you answer here again Christian 
Please let me know if it works fine for you.
In today’s release I added a new option to skip the domain validation for IPNs. This one could work well together with the signup vars fallback in some cases.
This release includes improvements to the fallback ipn signup vars and the domain validation skip.
Sounds exciting! 
They’re the ones I mentioned in this other thread: Cancellation notification emails stopped after hosting migration