My Vote
Global threshold as the foundation, set it once, forget about it for 90% of use cases. Above that threshold, show the big obvious warning I mentioned before: "Hey, this $2,400 invoice = ~$69 in fees. Want to do bank transfer instead?"
Per-invoice override (checkbox to disable online payment entirely)
User-level permissions (my accountant scenario - they can view but not pay)
Line item fees (for those who want to pass costs through - basically the same as adding a line item manually and calling it "processing fee." It's a dick move, but I ain't gonna tell someone how to do business the right way)
The permission thing alone would solve a future headache for me.
please let me know if this needs to be a separate request, etc.