Can you really hear the difference between different neck joints?

It's always good to challenge our assumptions, primarily because they are just that, assumptions. Not fact.
Neck joints have always been a point of debate but based mainly on subjective opinion.

Have a look at this article from Premiere Guitar and see what you think. You may be startled by the result.

This dude is one serious luthier and an engineer, interesting combination.

Yes, I used to have a bias against bolt on necks, but that was mainly because I owned a (very used) Fender Strat and every time I knocked the neck it would go out of alignment. The 1st string would then slip over the edge of the fretboard, on a neck that was (imho) made too narrow. I will never buy a Fender again; there are so many alternative makes out there (including Westone of course!) that are far superior, and way better value for money.
So - I'd say there are other things besides sustain that make one neck joint superior to another.

Sounds more like a loose assembly problem on your Fender than a result of the neck connection type. But it's true that when I was at the shop we'd see more than enough poor quality finishes and assemblies on name brand instruments. Inevitable I guess considering the sheer volume being produced.

But I gotta tell ya, my Mats-made bolt on's are the most resonant guitars I have, almost alive!