Just seeing if I am thinking this through correctly...

Seismic torpedo is an "Action:" effect, not a weapon. Rhymer's ability is "When attacking with a Secondary weapon..."

So that means Rhymer cannot use Seismic torpedoes to blast a rock at range 3.

Has anyone ever seen anything that would contradict this or seen a TO rule a different way?

Nah I think you're right. Seismic Torpedo isn't able to be used "When attacking" so it wouldn't work with Rhymer.

Correct. Secondary weapons are anything with the Attack: header, regardless of slot, and only those things, again regardless of slot. EM is not a secondary weapon, nor's Seismic Torp, Hot Shot Blaster and Snap Shot both are.