If properly seasioned maple is not in sort supply, then it might be the quality of the maple itself. Before the '70s, it was probably a lot of old growth wood, possibly air dried naturally over a period of years. After that, the wood isn't old growth and is kiln dried...that's a big difference.
I beg to differ about 1/4 sawn not being stronger than flat sawn. The grain's standing on end an a 1/4 sawn neck, MUCH stronger. Over the years, no. Fender necks are pretty good before the late '60s, then you see some necks with "ski slopes" or Rising Tongue, as Dan Erlewine calls it. Of course, the rod doesn't do anything that far up the neck anyway, so it's not a truss rod issue.
Almost every newer Fender neck I see with a vintage style truss rod at the body adjuster requires spacers because the rod has to be quite tight.
First, you're assuming your experiences apply to all Fenders. That's no more valid than if I assumed that no Fender necks ever had problems because I've never had one with a problem (and I bought my first one 49 years ago). Now, if we had a survey of authorized Fender dealers who do their own in-house repairs, and if they reported more Fender necks coming back for warranty problems than other brands, then there would be a known problem.
Fender never used old growth wood or air dried wood. You would have to go back to the 1920s or earlier to find either in large commercial quantities.
AFAIK most repair experts think ski-slope neck is a truss rod issue coming from years of the traditional (Gibson design) truss rod holding the neck fibers in compression for years. It's certainly not limited to Fender or to maple, and to say it didn't appear until the late 60s is just plain wrong.
Flatsawn vs. quartersawn: wood properties aren't subject to debate. You should download the Forest Products Laboratory (USDA) Wood Handbook: Wood As An Engineering Material
(link), especially chapters 3, 4 and 5. Wood strength tests are based on the type and direction of force applied, usually in relation to the grain direction, regardless of whether the wood is flatsawn or quartersawn.