No Programming via Native USB port possible on Linux

Because modem-manager listens on the DBUS if serial devices may become available. If one device is detected, which could be an modem, the modemmanager tries to identify and initialize that modem. When you told about that ~ 30s period it was suddenly clear.
I could have asked the question more early, but as I don't install modemmanager at all, I went that way down, I had to go myself.

Sorry for leading the long way round!