I have overpayed before, seeing my GFV figure drop as a result. I'm used to paying out £410 a month for my car and if the finance comes in at £300 a month with £2500 down and £14400 GFV then I overpay by £110 a month and have less to pay at the end (or greater collateral against the next one). The GFV drops not because the car will be worth less but because I will owe less on it. The true non-overpaying GFV quoted is a representation of the actual 3 year old value (albeit a cautious/worst case scenario one). GFV for base GTI is 51%, base GTD is 56%, actual true p/x values at 3 years old (if nothing untoward happens to the used car market in the meantime) is likely to be more, like 55% for a GTI and 60% for a GTD. Of course the GFV as a % will suffer the more toys you add on, seing as they hardly hold any value at all. A base 5 door manual GTD with £14400 GFV (56% retained) or a GTD with £3k of extras with a GFV of £14800 (51% retained).
In either case, GFV should not reduce just because you got a discount, that would mean that any discount you get is meaningless. Make sure your GFV is worked out on the list price and not the price you bought it.