You are given a range of meal plans and their ingredients and cooking instructions for the first month - you can pick which days you'll have a particular meal. On days that you'll be exercising ( 4 -5 per week) - you should pick certain options that have more protein/carbs.
Yes you can swap Joe's exercises for one of your preferred classes.
I don't think ready-made meals are allowed - purely because you have less control over what is put into them. That said - not all ready-made meals are the same - I had a quick look online of Itsu's menu and they seem to offer healthy options like salads etc - I would say if you pick sensible choices - it would be alright.
You are allowed to make your own meals based on the general principles of his plan. So (and don't quote me, because I'm just going off memory here) the plan might say - to have 30g of protein and 20g of carbs. So your 30g could be beef, chicken or vegetarian ....
However, a major part of the plan is preparing food in advance and freezing some of them for convenience to use later on in the week. So in theory, on the day that you would be ordering from Itsu - you wouldn't - because you'd have brought your lunch in with you
My own personal experience with the Body Plan was that I wasn't too keen on all the cooking - but that's because I don't cook much anyway!!! Didn't really lose anything at first (started around Feb/March) - but got a little fitter through doing the exercises - and to date have steadily lost just over a stone.