I’m replying to my own thread, for anyone else having similar issues.
After some investigation, we have noticed enabling hardware flow control (if your radio supports it) can help a lot!
However PX4 does not easily allow configuring it.
By default PX4 sets flow control to “Auto” which means it is trying to detect whether the device you are using is supporting hardware flow control, but as soon as a time out in MavLink communication occurs (which can already happens if you booted your AP before you started QGC for example), it drops hardware flow control and will not be enabled until the AP gets rebooted.
It is relatively easy to force enable flow control, when you know where to look. There is a module.yaml file in “src/modules/mavlink” add a ‘-z’ argument to the start command to force hardware flowcontrol.