Custom just means it's got non factory parts on it. You can build a custom bike with all bolt on parts. I mean an XS, or CB cafe racer that's basically just a pipe, ebay seat and clubmans is a custom bike. And atleast they got it back on the road. Lots of bikes end up basket cases when cost, ability and time don't work out.
Now a fully custom built bike is more than just bolt ons. Monoshock conversions, custom subframe for a tracker seat, tank swaps etc.
Suspension swaps used to be one off deals, but cognito moto changed that from only people who can make the parts to whoever can afford it. And those changes will continue to happen as long as there is a market. Same reason harley parts went from bars, bags and batwings, to ohlins and big bore strokers.
Unfortunately shows don't/ can't seperate bolt on customs from custom builds. So a shiny harley with the s&s catalog thrown at it will stand out to most people compared to an actual custom built UJM.