Wensleydale,
Just because MFTS is the way that UK flying training is to be carried out does not mean that it is not done on RAF stations. They are still RAF pupils being trained by largely RAF instructors in UK military serialled aircraft bearing roundels on RAF stations. RAF stations staffed by the regular RAF.
So that's Cranwell, Shawbury, Valley, Woodvale, Barkston Heath and just maybe Linton On Ouse to add to your list.
And there is no evidence at all that "The other bases are likely to close"
Just where would the RAF regiment go if Honington were to close? And Scampton, Boulmer, Leeming, Wittering, High Wycombe, St Mawgan are all rather full and busy, indeed some are having quite a lot of work done on them and their infrastructure.