DrewPeterson7
Sage of the Order
99.9% of the time, yes.
The one exception is that sometimes a frequency mod, to use your term, changes the way an amp breaks up, and you WANT to capture that effect. For example, a wah pedal is basically a foot-controlled filter control that really juices a narrow band and somewhat attenuates the rest. In front of a just-breaking-up tube amp, that can allow you to radically change the way the amp breaks up - listen to something like the solo Jimi takes on "Burning of the Midnight Lamp," where he's taking a gritty breakup and, when the wah is down to really juice the treble frequencies, pushing it in and out of saturation. It's a cool effect. Also, in the modern metal world a lot of guys put a Tube Screamer in front of a high gain head not for added gain but because it effectively acts as a pre-EQ, rolling off a bit of low and high end energy, and really helps juice the midrange frequencies (especially if you're boosting the volume as well).
But, when in doubt, yeah, unless you're after a specific tonal effect you're way better off just doing EQ tweaks in the mix so you don't have to get them right before you know what "right" is.
