having got a night train from paris to italy sans bike, i would just say that it's not like eurostar with passport control, baggage check, gates, etc, i don't think anyone even looked at my ticket until i was on the train...
It may be a bit cheeky but this may be one of those cases where it may be better to ask for forgiveness than permission. If you ask you will probably be refused or asked to treat it as freight in which case it may not even go on the same train as you.
I did take an unbagged bike through trains in Sicily once and but it was only allowed on about 50% of the trains (they had a little bike symbol on the timetable at the station)and you had to pay about 50% extra. I was travelling mid-day though.
A flexible bag will cost about £40 and if you take both wheels and handle bars off it won't be much bigger than a large suitcase. No baggage handlers to worry about but it's best keeping an eye on it if you leave it on a rack during the journey, just to make sure someone doesn't throw a 20kg suitcase on top of it. If you brought some heavy duty twine you might be able to tie it to the overhead rack depending on the size of the frame and the the rack. If you had seperate wheel bags these could be taken out and stashed elsewhere. I would get to the cabin first, get a top bunk and fill the rack before someone else does.
I've always thought if you look confident manhandling your gear rather than using trolleys you are less likely to get unwanted attention from conductors or other passengers.
Another option you may want to look into is posting/courier the bike to the hotel a week or two early and then posting it back at the end of your holiday. Never tried it, but bike shops seem to get cheap posting deals around the UK at least.
i've not looked into it but i've always wondered about couriering, always surprises me how cheap it is when i send boxes of documents, esp if not overnight.
i believe the going rate for a boxed bike in the uk (judging from ebay) is under 25 quid.
Couriers are relatively inexpensive.
The shop I used to work at sends stuff all over the world:
Forks as far as Japan and Oz.
Bikes to numerous locations throughout Europe. (about £150 for a Full Sus MTB)
Go for a large courier. This allows you to use the same tracking number for all steps of the journey. Most can be checked online now.
We used Parcel Farce quite a bit; OK in the UK but they hand over to a local partner overseas so the paper trail gets broken.
Clearly you must have somone you trust to sign for the parcel at the other end.
FedEx and UPS often have high street offices you can pop into: Maybe you could even send it to one of their offices and collect it there?
It would save all those hassles when changing trains etc.