Is it really getting that difficult? DS2 flew from South Africa to the UK aged 15.10 but this was some time ago and of course he was a British citizen/returning resident. He never travelled by himself in the opposite direction.
As for what he might get up to, if you can't trust him at 16, when will you be able to? And in reality, how can you stop him if he insists he's going? He can apply for an adult passport at 16, after all.
But I suppose I'm biased, because DS2 lived by himself from 16 and was absolutely fine.
I don't know for sure about hotels and such like, but some hotel chains in the UK - Premier Inn, for example - have a minimum age of 16, and Youth Hostels accept 16-year-olds as long as there are at least two of them. Since Britain seems to be more restrictive than much of Europe I wouldn't anticipate a problem, but best to check.
In my experience, immigration formalities are less of an issue for ferry passengers. (Possibly because they know for sure where you've come from.) I have never had my passport checked at St Malo, for example. That's France, of course, but there are no passport checks at all within mainland Europe so perhaps go to France by ferry and then train? Or possibly train all the way? (Eurostar to Brussels, then there's an hourly service to Amsterdam.)