The differences are sometimes audible. But in many cases they are not.

The difference in sound between single pole pickups and humbuckers is large - and I can certainly hear large differences between various humbuckers (the Jackson C90 being my favourite). There are also very audible differences between various single pole pickups, and there was a step-change in sound when individual pole piece pickups replaced bar pickups in the early 60s.

The wood also affects resonance - a Rickenbacker with its body cavities is instantly recognisable to the ear.

As with acoustic guitars however there is much irrationality. There are lots of acoustic guitars that may be preferred to and some that are outright better than the benchmark acoustic guitars (let's say the early 60s Gibson J-45 and the Martin D-45), and IMHO the status of the early Fender strats is as irrational as the lust for a '57 Ford Thunderbird (a truly horrid car) or a '66 Corvette (which I liked but can be outperformed by millions of Subarus today)