Japan Railways have high standards.

Brompton is the literal poster bike for JR "do's and don'ts."

I usually have the seat protruding from the rinko bag (it's a useful carry handle), but luckily nobody has cared enough to say anything, so far; it's more about keeping dirty chains and tyres away from people's clothes.

And yes, you can take a full sized bike in a bag, but it has to be no larger than overall dimensions of 250cm (L+W+H), i.e. partially broken down. Much more of a hassle than folding and bagging a Brommie, which only takes a minute or so, with practice.

Gods, I love the combination of Brompton x Japan. It's like they were made for each other.