Since some of the action is based on the materials reacting with organic matter, would there be a benefit to cleaning the tank as thoroughly as possible before treating? At least a good deep gravel vac for tanks with loose substrate.
An interesting idea. Though I'm not sure how much of an effect it will actually have on the treatment.
Flow doesn't penetrate very well into substrate, even if loose. For this reason, if you have algae growing on the substrate, I don't recommend turning it over prior to an algicidal treatment.
If you have lots of mulm on the surface of the substrate, then removing it would result in less H2O2 depletion.
Of course, if this is the case then a gravel vac is just good tank husbandry, regardless of treatment. Same goes if you have excessive buildup of mulm in deep substrate where there are no plant roots. No chemical treatment replaces proper tank maintenance.
On a tangent, sometimes I get buildup of mulm in the substrate visible from the front glass, in areas where gravel vacs aren't practical because there's plants and roots in the way. If it gets too ugly I measure out 2 tbsp. per 10G of H2O2, and inject it deep into the substrate along the front with a syringe, in approximately equal applications every inch or two. The mulm, broken down and more readily absorbed, disappears within a few days. You'd think this might burn the roots, but oddly I've seen no negative effects. Except for Marimo balls. Move them at least 6" away from the area, the prolonged exposure and high concentration will burn their bottoms.