Hello Marius and welcome to our forums,
Indeed it seems the previous workaround I offered it just adds a bogus entry set for the "managedRuntimeVersion" flag. I didn't catch this when I previously tested the workaround.
Anther workaround you can try would be to launch the appcmd tool to set the "managedRuntimeVersion" flag. Here are the steps to proceed with:
1. go to "Custom Actions" page and add a new "launch file" custom action with sequence
2. schedule the custom action to run after "Install Execution Stage -> Finish Execution" action group
3. configure the custom action like this:
- File to launch: [SystemFolder]inetsrv\appcmd
Command Line: set apppool /apppool.name: "MyAppPoolName" /managedRuntimeVersion:""
4. rebuild and test the package
Let me know if this worked.
All the best,
Daniel