Yes especially older models, if the car is not a run of the mill car, yes stock always wins over modified unless modifications are done with quality parts that are sought after on the particular car model and done tastefully, but if said car is with very low miles collector car condition do no touch with crappy mods.
Example
Buick Grand National,these things are very thought and desirable cars, these go from 8k to 20k in very good condition with decent mileage and engine mods, but if you have a ridiculous low mile example especially a GNX those go for lots of $$$$$$$ but they must be unmolested and have as much documentation as possible.
Same goes for run of the mill cars like older 90's Civics, find a stock unmolested one is like the holy grail, ive seen an unmolested all stock mint 90 CRX Si go for 12,000 bucks