Hi Kamil,
Can you check with your wintel team and have a script added after the deployment of the package to change the location of your saplogon.ini file where you actually want it to be placed.
We recently rolled out GUI740 using SCOM and integrated a script:
1. To change the registry setting for to overcome the security pop-up of allow or deny the connection
2. Have the service files updated of the end users with the sapms<SID> entries
3. Have the logon file created and placed and the correct location.
Hope it helps you to find a fix for your issue.
Thanks,
Manas