Yes, the flushing will indeed clean passages in the valve body and that's, of course, a good thing. But, that's not the whole or most important issue here.

A really gunked up transmission, as psfred properly pointed out, has its clutch surfaces basically held together with the crud. Chemical or pressure flushing can, and often does, remove the clutch lining material and renders the vehicle immobile.

Again, SMELL the fluid, before doing any kind of chemical or pressure flushing. If it is brown, not black and does not smell like varnish or turpentine, then change it and be happy.

Going to whatever length to keep an engine crankcase clean has no downside if done with good, common sense. This same mindset will NOT always work with an automatic transmission.

My $0.02,