Supposedly they may not scan as well as a normal biro, which is why they are not recommended. However, I would be very surprised if the scanning machine is so crude as to be unable to scan something written by a gel pen; this may just be a relic of the past when the technology wasn't as good. Worst case scenario, if it doesn't scan or something funky happens they will just request your physical transcript to mark, and your writing will definitely appear on that. As such, I would not worry about it too much.
If you go searching through other posts I have yet to have seen one where they wrote in gel pen and their work was negatively affected.