Actually - shooting a bare shaft and nock tuning is the "Best" way to do it. With a hooter shooter if you've got one to shoot bare shafts at distance. Think about it, all that matters is arrow flight, everything else is a method to get there, it's just not everyone's good enough to shoot bare shafts well and consistently or has a hooter shooter to do it for them, or has the time / space.
Guys like Tim Gillingham will build up a batch of arrows, and shoot every single bare shaft through paper and at a target (I think both?), turning nocks as needed to get the entire batch grouping together before fletching any of them.
Dudley just addressed this on a podcast. He basically says he buys .001" arrows, fletches them, and if an arrow groups outside of his others, he turns the nocks to bring it in. He mentioned on his latest 4 dozen, he hasn't found one he's needed to do that because the tolerances are so good.
Personally, I've played around with FLO but it hasn't made a difference, so now use a RAM spine tester with good bearings on the weight, check ends of the arrow for run-out as I cut them down and install the inserts, then I mark static spine, fletch and go shoot. With buying good arrows, they all shoot better than I do so haven't had one in my last 4 dozen that I've needed to turn a nock on. Not sure if that's marking spine, or more likely just good arrows.
If you really want to go overboard - buy a frequency analyzer. Even a step above FLO testing.
Frequency surveying instruments | GolfMechanix