Because you save a bloody fortune if you apply for them all at once.
How much do you save? Even if they waive the IR issue fee, that's only a saving equivalent to three holds on your IR training, hardly a fortune in the grand scheme of things compared to the peace of mind of having the licence in your hand.
Anyhow, I hope this situation is resolved without too much trouble for you, it's always a pain dealing with the CAA. I've never heard of them specifically wanting e-mail contact only, maybe that's new and a sign of things to come.
The public service counter can be quite a useful resource for getting answers and resolving things quicker, but it can also involve a lot of waiting around. At least the cafe does a decent lunch, even if they do make it clear you're being charged more for not working there!