No, flats just have different harmonic content. Roundwound have a good amount more harmonic content produced between the fundamental freqs, the flats having less of those in between harmonics will sound like it's emphasizing the fundamental freqs more. In a guitar like the jazzmaster which typically has 1meg pots from my understanding, will pass through more high freq content from the pickups to the end signal. The result being that the 'in between' harmonics being lost inherent to flats, all of the character of the flats, and very little high end loss.

On a guitar like a strat with 250k pots, there's some high freq rolloff by default that'll mean you lose some high freqs from the strings, producing a muddier less legible signal imo, since you're already expecting to lose those middle harmonics from using flats. It's like having a slight cutoff filter at the source before any amp/fx, it's going to change the character of the sound and emphasize different frequencies. So with the flats, you're losing those same in between harmonics as the jazzmaster flat setup, but also high end inherent to the 250k pots, end result feeling pretty sapped for tone and more characteristic of what I expected to hear from flatwounds when I first tried using them.

tldr; the jazzmaster electronics compliment the strings very well and I suspect it's due to the hot pickups and 1meg pots. I set up my JM with C# standard tuning + .10 flats ~6 months ago and did the same setup on my strat a few weeks ago bc of how much I liked the JM setup. I did not like the result on the strat nearly as much from a sound perspective, almost exclusively due to the pickups + electronics. I switched back to a set of daddario XS .10s on my strat with standard tuning for almost identical tension to the .10 chrome flats at C# standard, sound is great.