What makes a Ferrari better than a Kia? They're both cars and made from essentially the same materials.
In a well made custom cue there is a distinct upgrade in the quality of the materials used and the knowledge and craftsmanship of the maker. The better materials and craftsmanship do make a difference.
There is a lot more to making cues than I can explain but just as a for instance, the shaft of a well made custom cue is likely of old, aged, dense, tight grain maple. Production shops will not sit on wood this long to let it age nor spend the money to buy this kind of top grade material. The shaft is turned down by the maker in very small stages over what can take months. And you better believe this makes a difference in the hit.