It was because of 45's seniority - at the time of the TWCU formation, it'd have been about 19th on the list of seniority, whereas 35 was approximately 52nd and 50 was around 90th on the list.
45 was the most senior numberplate not in use at the time. Although the rules/policy permitted another numberplate to be used for a reserve squadron if there was a good reason for it (e.g. 76 Squadron's reformation as a Tucano unit at L-O-O because of the association between the squadron and LOO during the war), 45 was senior and had 'role association' having served in a number of different roles during its existence (fighter, fighter-bomber, light bomber, ground attack), making it appropriate for the MRCA.
The approximations are because I'm using the 1973 list and there is a possibility that, post Hunters, 45 would've slipped a place or two, while 35 and 50 might have moved a couple as some squadrons just ahead of them in the list had disbanded, enabling 35 and 50 to overtake them through length of accumulated service; there was often very little between units at that time, and short periods of disbandment could allow squadrons to swap places in the list.