I wouldn’t say that you’re alone playing with a controller on PC. The game feels really good with a controller, and some wonky targetting aside (teleport, some AoE spells), it’s fluid enough for me to achieve high level content anyway. I’m couch gaming, and with an history of carpal tunnel syndrome, a controller feels better over longer sessions compared to KB+mouse. So no, you’re not alone.
With that being said, I think that your issue is tied to a Steam/Battle.net interaction or something. I play with the standalone (battle.net) client with one of my Xbox Series controllers, and I don’t have any issue.
What’s worse is that you cannot simply install the Battle.net client and forego Steam to get rid of the issue. I hope someone at Blizzard sees this and help you.