I think it's mainly to aid regulation at Haywards Heath. Most of the 1Wxx / 1Mxx GatEx trains are scheduled to overtake a 9Txx / 9Sxx Thameslink service at Haywards Heath. Allowing the signaller to easily distinguish the GatEx 1M/1W that's overtaking from the Southern 1A that's stopping is probably quite helpful when something's a little bit late.
Furthermore, the extra GatEx trains in the morning and evening peaks that stop at Haywards Heath are headcoded as 1M9x (morning) / 1W9x (evening), to distinguish them further (all the other 1M/1W have numbers 00-89).
There has also been a move towards trying to make headcodes unique across the day, wherever possible; with all the Victoria-Brighton trains being 1Axx there would have to be two or three trains across the day with the same headcode. This way, there are no duplications in the 1Axx range, though there are still some duplications in the 1Wxx and 1Mxx range, so it doesn't completely fix the problem.