A set neck is far superior for both acoustic and electric guitars. Tonal purity and the lack of interruptions in the wood on wood contact areas create the best sound qualities period. That's not to say your taste leaning towards the bolt-on neck's tonal properties on a Strat makes you wrong versus the love I have for the deep sustain and bite of my semi-hollow Les Paul Doublecut, but that we interpret the sound differently (which is the best part of guitars/guitarists.) But if I am searching for the best possible sound for a certain body shape, using the same top/back/side/neck/fingerboard woods, etc...a set neck will always provide the absolute best sounds. Everyone is different and hears things differently but it is what it is.
Feedback is gained in much better ways than relying on a bolt-on neck, and you're right, not desired at all in acoustic playing. This is especially true on mic'd acoustics. But I really don't believe the bolt-on necks contribute much to the feedback or lack thereof of an instrument in comparison to a set neck.
In my teachings and personal experience, the only guitars in general that are any more work in regards to refrets are guitars with old and dried out rosewood fingerboards, or any guitar that has a bound fingerboard (especially Gibson's as they cap the end of the fret with binding. See image below.)
Also, it does depend on the type of fret installed on any particular guitar, especially of age. But a refret always requires care and concentration regardless of the make or model, especially on a customer's guitar. I believe it was Fender that originally fretted guitars from the side using a press instead of pressing them straight down into the fret slot like everyone else. A guitar that had frets inserted this way could be fucked up easily from a repairman that didn't anticipate it and tried to remove the fret in the typical manner. This could be even more disastrous on a guitar with a maple fingerboard as maple requires a finish unlike a rosewood fingerboard. A simple refret could lead to wider fret slots and a respray on a maple fingerboard among other things. Probably a good thing they eventually killed off the idea in favor of the traditional method.
Mod list on the Strat? I have a 50th anniversary Standard Strat (made in Mexico) that I've had for 16 years, it's all stock and sounds ok, nothing like a real Strat unfortunately. but would really love a David Gilmour signature, or a 1969 Custom Shop 3 color sunburst Strat to outfit with the EMG Gilmour pickguard/pickup setup...maybe someday.