noise will be part of the picture =) , i've come to terms with single coil hum/noise on loud cleans/or overdrive tones , especially with my small pedalboard (no gate on there) into a vox ac10,a noise gate on there would also mess with things i imagine
the way i setup my fractal presets , i keep the gate in the input block turned off and use a separate gate if needed that i place usually after amp/cab but before delay/verb etc.. a bit like within an FX loop
however i only tend to use a gate for big hi-gain/metal applications, or stop/start sort of playing, where you want things to mute between passages , which is what a gate can do perfectly, for lead scenes even with hi-gain, the gate is off, so no gate kicks in on decaying notes
for cleans/edge of breakup and maybe low gain tones, i don't use a gate, but this is true to 'real world' setups that i would also use,
as to the gate messing with the feel, it's maybe more how the settings of any noise gate clamps down/closes on noise depending on the settings
and how quickly it does that, playing around with attack/release can help (ie. slower attack/release), maybe placing it later in the chain and trying out the sidechain input option as well, could be some ideas, ultimately you're setting things up for how things best suit you