This has been driving me crazy as well. I disabled the app in the Login Items, yet I kept seeing this dang popup. I spent a lot of time researching launch agents running on my system and finally found the culprit: Elgato Stream Deck!
Elgato is owned by Corsair and it turns out they are saving costs by using a single Apple Development team for signing their applications. This can be seen by viewing the signing certificate associated with the Stream Deck application:
$ codesign -dv --verbose=4 /Applications/Stream\ Deck.app
Executable=/Applications/Stream Deck.app/Contents/MacOS/Stream Deck
Identifier=com.elgato.StreamDeck
Format=app bundle with Mach-O thin (x86_64)
CodeDirectory v=20500 size=105537 flags=0x10000(runtime) hashes=3289+5 location=embedded
VersionPlatform=1
VersionMin=658688
VersionSDK=721152
Hash type=sha256 size=32
CandidateCDHash sha256=ae4a3d15bceb92cfea0c7f2b1d2f87557f2063c2
CandidateCDHashFull sha256=ae4a3d15bceb92cfea0c7f2b1d2f87557f2063c2df36b705df9bea2f52a162ce
Hash choices=sha256
CMSDigest=ae4a3d15bceb92cfea0c7f2b1d2f87557f2063c2df36b705df9bea2f52a162ce
CMSDigestType=2
Page size=4096
Launch Constraints:
None
CDHash=ae4a3d15bceb92cfea0c7f2b1d2f87557f2063c2
Signature size=8976
Authority=Developer ID Application: Corsair Memory, Inc. (Y93VXCB8Q5)
Authority=Developer ID Certification Authority
Authority=Apple Root CA
Timestamp=Sep 29, 2022 at 6:54:05 AM
Info.plist entries=28
TeamIdentifier=Y93VXCB8Q5
Runtime Version=11.1.0
Sealed Resources version=2 rules=13 files=527
Internal requirements count=1 size=184
So this is safe to be running if you installed any Elgato software and want it to run in the background on login.
I couldn't find any settings within the app to disable the auto-start behavior. So you can manually remove this launch agent to prevent it from running in the background:
sudo rm -rf /Library/LaunchAgents/com.elgato.StreamDeck.plist
sudo rm -rf ~/Library/LaunchAgents/com.elgato.StreamDeck.plist
I confirmed removing this file does remove the item from the "Allow in the Background" list. This file gets installed when installing the app. So it won't return unless you update or reinstall the app.
If you want to allow the app to open on login, just open the "Settings->Login Items" and add the app into the "Open on Login" list. This will open it in the foreground, so you just need to close it after it opens.
Not ideal, but it removes the annoying popup. Hope it helps!