When I took this flight last month I asked the same question. I was told it was because of a number of reasons. The main one being that BA needs to keep a presence at T3 so they have lounges and ground staff. This could become more important if or when more flight come from LGW.
Apart from that I am unable to think of anything.
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BA Gold, BMI Gold, UAL PE, Hilton Diamond, Freeloader...