I've had the "App detected on Secure Desktop" pop up trigger. That pop-up is usually delayed by a second or two. (At least when triggered by fresh Synergy installs.) It's quite likely that the user will be typing their master password in when the pop-up appears. If the user presses "Enter" to submit their master password as the pop-up appears, but before the user has noticed it, the "Enter" will be directed to the pop-up, selecting an "unknown" (to the user) button from that pop-up.
The "App detected on Secure Desktop" dialog should not have any of it's controls gain focus when it appears to avoid accidental input.
Focus being lost from the master password input control is probably a good thing from the security stand-point, so it should probably still happen.
1Password Version: 7.4.759
Extension Version: Not Provided
OS Version: Windows 10 Pro Version 10.0.18363 Build 18363
Sync Type: Not Provided