Avanti still do ‘Tilting Ale’.
It was discontinued for a while, round about the time of the franchise change if I remember correctly, but has since been reintroduced. Produced by Redwillow brewery of Macclesfield.
A while back (several years) there was a guest ale on at the Head of Steam in Huddersfield called Northern Pacer. Can't remember the brewery (think it may have been Ringwood) but it was a light ale at 2.8%abv. Not available on trains though, so it doesn't qualify for the thread but thought it might be of interest. A shame it wasn't available (as far as I know) on the Penistone line Music Trains.
That one was made by Hopback Brewery. A quick Google search suggests it was prevalent across the Head of Steam outlets at one point.
A brewery in Scotland produced a Flying Scotsman beer some years ago.
That was made by Caledonian Brewery, formerly of Edinburgh. I think the beer might still be available, now brewed under licence by Belhaven.
I've not seen any operator-only brews apart from the ones listed. There used to be a served-in-First-only Tilting Cider on the WCML, I don't know if that is still a thing but it was very refreshing!
I seem to recall that the Tilting Cider was discontinued before the end of the Virgin franchise. Pity, as it was produced by Dunbar-based Thistly Cross, whose cider range is generally superb. Though could still be available in First, I'm only really aware of what's available for The Shop these days.
(Ah, beaten to it on a couple of counts while composing my post!)