It seems like your forgetting that the CR system, while great and very useful, has always been broken when you start adding things on top of existing creatures. By your own admission CRs get wonky when you start adding templates onto creatures. Well mythic is just another type of template, and you should treat it like that. Namely, that the CR adjustments as written are flawed and as a GM you need to account for that just like you would if you put 2-4 templates onto a normal creature. It's not a good thing that it's flawed like this, but it's nothing unique to the Mythic rules and you shouldn't treat it that way.
Also, it seems you're forgetting how over the top Hercules actually was. Hercules didn't fight roving gangs of 4-6 goblin raiders, he fought entire goblin warbands on the march. So yeah, if you throw a fight at a mythic party the way you'd throw one at a non-mythic party of course it's going to be trivial. Even at level 1/mythic 1 throw armies at the players, with mythic as written they can take that and that's kind of the point. The only real way non-mythic enemies, even CR appropriate ones, are going to hurt mythic players is through attrition. (I'd also suggest playing on the slow exp track so they don't level up crazy fast)