Flybe have operated Dundee-Jersey flights for some time - why would they be any different? And Flybe has operated into plenty airfields without controlled airspace for years - e.g. Exeter and Newquay.
OK Dundee has no radar but commercial flights get a radar service from Leuchars down to 2000ft if necessary and non-transponding traffic has no impact on that.
There have been no airproxes of any sort anywhere near Dundee this year. So I'd be amazed if it was anything to do with the amount of light aircraft in the area.