Originally Posted by KevinB
Just to add, I have built a Tele with a Strat neck using a Strat-shaped neck pocket route. It sounded absolutely nothing like a Strat.
My belief is that it's all about the bridge.
It is totally about the bridge. A strat trem routing takes out a ton of wood, and is configured totally different from a tele bridge. If it's floating, the difference is even more extreme. Also, anchoring strings into a trem block attached to springs, vs. anchoring them into ferrules in the back of the body, is going to make a large difference too. Both bridges have different weights and masses as well.
After a lifetime of working on and playing guitars, I would certainly attribute the biggest tonal differences to the bridge systems. If, as the OP said, pickups on both guitars are identical. Also, I would give some consideration to headstock and body mass.
I would give zero consideration to the neck joint. if it's well made, a bolt on maple neck is a bolt on maple neck, is a bolt on maple neck. I called Warmoth, and they agree with me.