One example would be an ARC Ref 75 being upgraded to a 75SE. Is the upgraded version inferior to an original 75SE?
In this example I would say that though the upgraded unit may sound the same, the original 75SE will have greater resale value on the used market.
Why? Because in the upgrade process, only certain parts are being upgraded, not the whole amp. So if you are buying an upgraded used 75SE, 70% of your parts may be a couple/few years older than a used original 75SE.
Outside of that, there are qualified modifiers outside of original manufacturers. Folks like Steve McCormack, Chris Johnson, Bob Backert, Bill Thalmann, and others who perform modifications outside of the original manufacturer. Many of these certified modifiers products may idea sound better than the original. However, you will lose about 80 of your modification investment on resale.
Then there are other lesser qualified modifiers (all DIYers), whose work actually devalues the original product on the used market.