I guess it depends on how and where you ride and what you consider acceptable... the only time I want / need to touch my wheels with a spoke wrench is when I have to take them apart because I have worn out the rim.
This is how I build wheels for myself and customers... I also tune machine built and factory wheel sets for people.
Machine built wheels can be good too... but I would not take them off the peg and ride them with an expectation that they would hold up.
Just serviced a set of factory wheels with 1300km on them with no pre-service that were suffering from tension issues and were out by as much as 45/1000 on the front... the rear tensions were way off.
These were on a $1000.00 bike.
Besides all this I am now building frames and every bike that rolls out of our shop has hand built wheels and we aim for a build tolerance of 1/1000... they also come on hand built hubs that are guaranteed forever.
So are custom wheels worth it ?
I would say yes.
Amortize the cost of these over the life of your bike and factor in the peace of mind you will have when you know your wheels can handle anything you subject them to and the extra cost becomes a saving.