What exactly is your concern? It really does not matter where, or if, you get your passport stamped as long as your travel details are logged in the respective tracking systems.
From what I have gathered so far, you might get checked and stamped as the bus gets off the ferry or train...or you may not, some check and official review will be done, but unless someone has taken Flixbus recently, it is impossible to say definitively what form that takes.
Returning from Amsterdam is no issue, France, Belgium, and the Netherlands are all Schengen countries, so for most Nationalities that is handled as a single entity. On return to the UK, you will go through some type of Immigration again. If you happen to be from a Country where you need a specific Visa for a Country (ie: not USA, Canada, Australia, others) and this question is related to your Visa, then this is likely not the place to ask.