Just to clarify a few things here -
All of the large integrators (TNT, UPS, FedEx, DHL) perform pre-Customs clearance well in advance of the flight landing in the country. All the details are submitted by the carrier to HMrC and when the plane touches down (wheels down) that is when they receive the message back from Customs to state whether to hold or not for examination.
It is not customs who look and see if something is supposed to be charged Duties/Taxes but the carrier in the main part. Customs will only scroll the manifest and look for any suspicious items or anything else they may be interested in.
A carrier has a responsibility to ensure that all D&T's are collected and paid correctly - and will be fined if they regularly allow shipments through without payment.
All D&T's are calculated based upon the value and description as provided on the commercial invoice. The description is as important as the value - as different duty rates are payable on different commodities - and due to the vast number of commodity codes - an item can be classed as different things by different operators.
Eg - If you order a Wheel Bearing made from Steel from the US - dependent upon what description is supplied on the CI then that could alter the amount of Duty you pay.
It could be listed as "Automotive Bearing" or "Automotive Wheel Bearing" or "Generic Car Part" or "Bearing made primarily of Steel" or "Steel Machine Part" etc etc
Each of these could (although I havent checked in this example) attract different rates - so its dependent on what the employee who is doing the pre-clearance classifies it as. It could be "zero rated" (ie 0%) under one category but 20% using another.
None of them would sting you for HMrC charges that they hadnt had to pay themsleves - They may however charge a "admin" or handling fee. This is to cover the cost of the operator doing the clearance work and submitting to customs.
VAT is, in the main part, chargable on everything imported into the EU - and is charged on the "CI Value + Duty" at the rate currently in use
Finally - Mis-declaring an items value is a criminal offence and therefore not advisable - It is exactly the same as walking through the Nothing to Declare channel when reterning from outside the EU - knowing you are over your limit.