The reasons in favour of the 350s being taken to GWML, would need to be balanced.
During the course of the day, you need 12 units for the Didcot Parkway to Paddington services, assuming 8 coaches.
You also need 3 units for the Newbury to Paddington, which runs as a 4 car but has a 62 minute turnround at Paddington.
A further 2 units for the Newbury to Reading shuttle.
Unless I am missing anything, that's only 17 units. Even bolstering capacity at peak, and adding in any odds and sods, that's all there is. I doubt the Cardiff diagram is absolutely mandatory, but if Swindon drivers are the ones who are doing it, then they'd be signing 350s anyway as they already do Didcot to Paddington work?
Electrification to Oxford is not happening soon. Nor is Reading to Basingstoke, or anything like Newbury to Bedwyn, or the branches. So you're actually net gain, with the option of an increased use of 110mph 350s on other services as required (perhaps some Cardiff diagrams, perhaps in that way), to release more 80x fleet back for longer, better services between Cardiff and Bristol, or out West.
Quite bluntly, Heathrow Express is also not important. If you have to retain a microfleet of 387s for a short period for that service, then so be it. They will undoubtedly get replaced in due time, and the service may even fold.
So, all this in the round, this seems fine to me. And in return, you are sending a small heap of 387s with DC shoes off to be able to partially reshape the Southern route, homogenising the 387 fleet in Sussex. Or, you end up simultaneously replacing the Southeastern fleet in totality, which gives Southern plenty of units to choose from e.g. 377s, 387s and you can then start considering battery fitment if that's a serious idea for the Marshlink and the Uckfield, and possibly even the North Downs if you switch operators.
I don't have a view either way, but I don't think there's much reason to keep all those 387s on the Western, when you could potentially use them on all sorts of other services south of London.