You're in the clear
Official Customs, Duties, and International Shipping Questions and Stories Thread - Page 5
In my experience Royal Mail is fine. It's FedEx and UPS that you have to worry about. Of course it sounds like it all depends, but generally the post office doesn't seem concerned with customs oddly enough.
As for VAT, you probably should have sorted that before ordering. I had a sizing question from them over the Summer and got a very quick reply, so you might want to reach out. Some places (Coggles, Liberty) don't deduct VAT at all (which is IMO complete bullshit and reason to never order from them).
Can you elaborate? What I can tell you is that Superdenim does mark down the value of the package, they have for me every time and that includes an order of 4 pairs of McNairys, and shipping is quite fast. Can't remember the carrier they use, but it's fast and they mark down the package. 3-4 orders last year and never been hit with customs.