Seeing as the LM20 is a modified Litchfield car, further Litchfield mods shouldn't really affect the value? It would be like optional Nissan extras.
It brings you onto what makes a "limted edition" car.
The LM20 is an awesome bit of kit but long term modded or not, is it a true limited edition in terms of future values as rare?
It's a standard car that is aftermarket modded to a set spec, which constitutes the limited edition status.
I personally can't see them retaining a huge amount more value over a standard car modded to a similar spec because they are not a manufacturer limited edition car. And therefore extra Litchfield mods wouldn't bother me at all.
For me, when I got mine, it was a new GT-R with mods that had a similar warranty to Nissan including the extra bits. That was the main attraction.
At 3 years old next year they will have an equal warranty to every other modded GT-R out there. None or one you pay extra for.