The original question still holds good...How would he have got on the aic without a boarding pass, to get inside the loo?.
Think about it, he's an eleven year old and it's the start of the school holidays so Terminal 1 is packed out with families and groups. Kids often aren't trusted to keep hold of their own boarding passes and passport, which is entirely sensible. The lad mingles with different families from airside to the plane and they think he's just ahead of/behind his own family, or something like that.
As I mentioned before, Manchester Airport no longer has dedicated staff checking boarding passes at the entrance to security, it's done by busy screeners who aren't necessarily in a position to thoroughly check each child in a large group (they might not be able to see them even).
Boarding the plane, mum/dad hands over boarding passes and passports to the handling agents and later boarding pass stubs to the cabin crew, this lad meanwhile mingling in with these families who perhaps aren't paying as much attention to him as they should.
Jet2's policy was that no headcount was needed, if the aircraft had been boarded via an airbridge directly from the terminal. All UK and Ireland based airlines the cabin crew have to check boarding passes, but headcounts are not compulsory. However, many countries don't have that requirement either.
Jet2's policy was not slack at all, since British Airways currently does not routinely perform headcounts either in these circumstances. Not that the media would tell you that. easyJet and Ryanair have compulsory headcounts on all flights (then again, the latter avoids airbridges wherever possible) and this incident may result in this procedure becoming mandatory on all airlines.
Good will come from this is the long run, lessons are bound to be learned and we will all be safer for that.
He was fully screened by security staff, so judging by the current standards he no risk to the aircraft. If he'd evaded being scanned, then the Airport would have been in massive trouble.
It's not terrible uncommon for passengers to end up boarding the wrong flight and only noticing when the destination/flight number is mentioned!