I often get the train and it's almost always fine.
I think it depends on the experience of the 'line' you're on and the accompanying staff etc with it. It sounds like you're planning on using lines that are probably used quite often by mountain bikers so the staff will be used to it and will take a common-sense attitude. I've never ever been reprimanded for being muddy and I've got on the train in some right states before now.
The only time I've ever had a problem was coming back from Bolton to Manchester on the last train home. I'd just finished a race and was done-in, so cycling was out of the question and plus it was pitch black anyway. I saw the train manager and he told me to put my bike on the bike carriage but when I looked I couldn't find it. I started to panic that the train was going to pull off so I just got on and stashed my bike in a doorwell alongside another lady who had her commuter bike there too. When the train guy saw me he went off on one, shouting how he'd already told me to go to the bike carriage etc. When I explained I'd looked and couldn't find it and was scared the train would leave without me he told me to use my 'common sense' which annoyed me a bit as despite being in the wrong I don't think I'd omitted to use 'common sense' as I was out the way and stood next to my bike ready to move it if needed. When I told him this he threatened to throw me off which unfortunately carries some weight when you're on the last train home in the dark, and don't know where you are. Had to apologise like a mug in front of smirking passengers which was hard to swallow.
Have to say though, that was the one in one-hundred time where I've ever had any trouble, always been fine otherwise.