gnome terminal running bootstrap-agent irritates tests

Distro specific autostart scripts in /home/qt launch
/path/to/gnome-terminal -e "/home/qt/bootstrap-agent /dev/ttyS0"

The command starts the bootstrap agent in a terminal that stays on top (due to the -e option?).
Additionally, the output of the bootstrap agent is sent to the first console and piped to /home/qt/bootstrap-agent.txt.

The terminal staying on top irritates tests using the graphical desktop and causes flakiness.