It sounds like you were several versions behind on updates. These changes were covered in the release notes on the downloads page here: https://www.simxperience.com/downloads

The issue you are experiencing is more a limitation of iRacing and we have a solution for it. The specific document you are looking for is here: Launching Games in VR

There is a section in that document called special notes about iRacing

Bottom line, we're damned if we do and damned if we don't. We want to provide the ability to launch games to screens or to a particular headset. iRacing is special in that it persists the settings to disk. Other games don't do that. When we made it so that it didn't prompt when you click the Launch button, users who didn't read the release notes complain because that's the iRacing default. When we make it the iRacing default, users such as yourself who don't read the release notes complain. I can only chalk it up to the price of progress.

EDIT: It turns out that this post was related to a 3rd party utility that also wants to modify the iRacing ini file VR settings. Version 4.2.66.0 was published for download. It may help to better co-exist with some utilities like this if you were to launch from the other utility tghen start the profile from Sim Commander. None of this is suggested for a typical Sim Commander user because you will lose a fair number of Sim Commander features/capabilities by having something else launch the game. This is because there are many things that we need to do before the game is launched and we can't do that if we aren't launching the game.