On the whole we haven't come across schools being deliberately obstructive (which is not to say that it doesn't happen sometimes).
1. The non offer letter did not refer to an appeal process at all. I understand this contradicts the Code in para 2.5 (2012 on edition).
I agree that, if parents are not being informed of their right to appeal when a place is refused, then para. 2.5 appears to have been breached.
I assume that in practice you've not been disadvantaged (as you've had an appeal), but you could still consider complaining to the EFA. http://www.elevenplusexams.co.uk/appeals/ombudsman#d6
Unless they have a very good explanation, the admission authority is likely to be reprimanded.
2. The school would not reply to sensitive appeal related emails with the original email attached, but start a fresh email in response, this would leave the parent having to convince a panel of the connection if any valuable information arose out if this. The school would however be happy to attach original emails when dealing with not sensitive emails.
I think someone would need to raise a specific instance of where they may have been disadvantaged.
3. In a case of a very time sensitive email, it was answer three full days late, which went against all previous replies of no more than 1.5hrs. The information requested was not difficult but did include questions on net capacity and staff numbers (which would have helped in our case, but was not presentable at hearingf due to lateness). My email to the school stated clearly our appeal date and I am in no doubt the admissions people would have checked and chose to reply after the submission deadline.
If information was received late, I would have thought
(a) the clerk's notes should show whether the panel properly considered what to do, e.g. whether an adjournment would be necessary, and
(b) that you should have been told of their decision. (However, if they said nothing, it would be a reasonable assumption that the new information was considered, and the clerk's notes ought to show what view they took of the evidence.)