Welcome to Flyertalk and welcome to the BA Forum.

For the AUP with Avios option, yes you were correctly charged. The Avios option is just a lookup against the cash rate, and it's not a good rate of exchange at all - just about the worst use of Avios in my view. But had it been a cash upgrade, which is better value for money unless you really can't get rid of Avios any other way, then the cash upgrade still doesn't take account of the Companion Voucher. Had you been able to do the upgrade before travel, before getting to the airport then the Companion Voucher would be taken into account.

For EC261, there is a dedicated thread for that, and you will find this thread, and similar useful threads, via the BA Forum Dashboard. But the short answer is to go to CEDR at 8 weeks regardless. You may as well get that going sooner rather than later.