Way overhyped.

Look around you; 99.9% of bikes are rolling on factory stock wheels. How many failures do you see? and look how many old wheels there are around, having spent years getting slammed on sidewalks.

For the .1% of riders who have particular desires or are particularly discerning or particularly demanding, then yeah, custom guilts can make sense. Maybe they want a particular rim, a certain color combo, or the lightest wheel...these are reasons for a custom build.

Durability is not.

That said, if the bike is not spec'd to meet your expectations, e.g. it's a superlight race that you want to ride daily on ****ty roads while loaded with panniers, you may want to consider a beefier wheel build, but be aware that there are plenty of off-the-shelf, pre-built wheelsets perfectly suited to that purpose which are likely going to be cheaper than the LBS custom builds.

Stock vs Custom, factory vs handbuilt....it's not the same world today that it was twenty years ago, and the old paradigms--and their contingent trade-offs--don't accurately sum up the situation today, IMO.

For example, are a $280 set of USA handbuilt Velocity Aeroheads better than an $800 set of factory Mavic Ksyrium Elites? Are they lighter? More aero? More durable?

Despite being handbuilt customs, the answer across the board is No.