An EtreCheck report tells that my app is not signed, while codesign -dv /Applications/***.app returns a valid signature. I'm lost...
EtreCheck isn't designed to be used with developer builds of apps. It only considers Developer ID and App Store builds as valid.
You should consider spctl the authoritative result. Years ago, I used to use codesign more and I would test a Developer ID build with "codesign -vv -R="anchor apple generic" /path/to/app".
However, you also mentioned TestFlight. I've never used TestFlight, but isn't that an App Store thing? So are you doing developer-signed builds? EtreCheck has no idea about that.
Never attempt to disable Gatekeeper on your developer machine. That would be a bad idea. Thankfully, Apple recently added an extra hoop to jump through that saved you.
I'm sure your Sequoia install is fine. It's the app that's corrupt. I was confused at first when you were talking about Monterey and App Store. You need at least Ventura/Xcode 15 for App Store submissions. I guess you are using Sequoia only to submit? I think you're just hitting some odd edge case on Monterey.
My recommendation is to build and debug on the oldest supported configuration. As of right now, that's Ventura/Xcode 15, but that could change any day now. Then test on any other supported OS versions, heavily favouring Sequoia and Sonoma.
There is one developer feature in EtreCheck. Look at EtreCheck's "Operating System Adoption over Time" page in "Insights". Sequoia is 66% of installations. Monterey is still holding on at 9.1%. Anything before Monterey is a waste of your time unless you have a very specific user base.
If you post more details about your app, then maybe someone could see what's wrong with it. Maybe disable any DRM and build a notarized Developer ID version and fully test that in a VM. Make sure to actually download it from somewhere so you get the correct quarantine flags.
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