In the early 2010s I worked for Fiserv, who at the time provided "online bill pay" services to about 80% of US banks (I don't recall if they're in Canada or not). The overwhelming majority of the bank customers using that service held beliefs similar to what you expressed... it's an online payment through my bank, why on earth would it be a paper check?? They were wrong. The really fun thing about that system was that the customer had absolutely no way to tell what kind of payment the system was going to send to a given payee. A payment that processed electronically for years could suddenly go as a physical check for any number of reasons. Maybe the customer changed something that was slightly incorrect... maybe they should have changed something but didn't... maybe the system just had a hiccup that day.

Regardless of who makes your bill pay service or exactly how it works, my main advice if you use any bill pay service is to ready the fine print very closely and be sure you understand what you have to do to be covered (late fee reimbursement, etc) if a payment does get screwed up.