If one looks close enough, all sensors have noise at all ISOs regardless of the comments by the fan boys. When someone doesn't see noise until above ISO 6400, they are just looking at very small images from a distance, perhaps on a low resolution monitor. View at 100% on a 4k monitor, up close, and the noise will be visible.
There is no magic here, Capture One vs Lightroom is just a matter of your choice of settings and adjustments. Noise is inherent in the sensor technology and not Bayer vs X-Trans. Because of the arrangement of the color filters on the pixels, color (not luminance) noise is affected. Some colors will be noisier with Bayer and others noisier on X-Trans.
With my X-T1 (admittedly less noisy than the X-T2 which is less noisy than the X-T3 though not by much), up to ISO 3200 only modest noise reduction was needed. In Lightroom, 0-10 for highly detailed photos, perhaps 20-30 with smooth areas like the sky, especially a dark sky.
The problem is that the camera companies listen to the pixel peepers (overwhelming majority) and not photographers. The highest IQ sensors from Canon, Nikon, Panasonic and Sony are all their lowest resolution models.
Want lowest noise and highest IQ, pick up a Nikon D3S or the almost as good D4/D4S. At ISO 6400 they are superior to our Fujis at ISO 800. Expect to pay $1500-2500 for ones in excellent condition. But this is a discussion for another day.