i had rust on the boot of my cab it was where moisture had causes rust along a seam and that eventually went through.
I cured it by sand blasting the rust to bare metal, leaves a completely rust free patch size of a 10p coin, grind any remaining rust out, apply filler and spray.
i removed the bung in the bottom corner to allow water out and sprayed the inside of the panel with wax oil as this has rust repellents. That was 8 months ago and nothing as come back, before that i just rust treated and touched up the rust, it came back a month later.
garages due to time and expense will remove most rust and patch the panel up, they dont have the time to shift it 100%.
can you try and remove most of the rust yourself and let the garage touch it up then, atleast you will know there is bare metal there. if its only just started its taken 10 years to do so treat it right and it should last another 10
if its a water trap in your make sure there is no crap behind the panel that may absorb water and trap it for a period of time.