Shoemaker:
There is not a single answer to all the issues you raise and unless your name is Robert "Shoemaker" Maxwell and have access to other people's money, no answer which will give you much comfort. I hope that you are big enough to accept a response mainly for the benefit of others.
The tradesman's behaviour is typical of that featured on BBC Watchdog "Rogue Traders". If you are familiar with the programme you will know that obtaining monetary redress is almost impossible.
The fundamental problem is that an "emergency electrician" has been used for a problem (bedroom lights) which arguably is "not an emergency". There is a big premium to be paid for "emergency" response - even when it is tardy, or perhaps that should be especially when it is tardy. A better solution would have been to contact a local electrical contractor registered with a body such as NICEIC.
I can't specifically address the £242 without knowledge of the itemised breakdown, but given that the lights presumably were previously working, probably the remedy didn't *require* a junction box unless the fault was inaccesible (something which can't be completely excluded), and anyway for an emergency electrician not to have a junction box in the van is just an excuse to charge for a trip to the merchants at "emergency" rates. An expensive junction box.
Had you used an accredited contractor the failure to replace the ceiling light covers could have been taken up with the contractor under threat of reference to the accrediting organisation (NICEIC typically).
The "missing earth" would not have been provided (or charged for I hope) unless you asked for the work to be done. Similarly if you want "certification" you need to pay for a Periodic Inspection Report or PIR. Neither is work which should be entrusted to an emergency electrician.
The "lights flickering" is just possibly related to the original fault. Do you know any competent DIYers who could help with tracing the cable which causes the lights to flicker?