Today I chatted with a customer who was having issues with the DBUpdater tool, because this console app displayed a small splash screen even if it was run in the silent mode...Sounds very familiar? Yeah, I saw this myself in the past a few times and I knew that this small icon appeared because DBUpdater setup XafApplication internally. After a quick search I found that I even logged a suggestion on removing this icon:

DBUpdater - Remove an application splash screen showing during the database

Good news is that it was not too hard for me to finally fix this today. So, in 12.2 everything will operate as you expected.