If the main team of Dino Charge Rangers were going to be counterparts of the 100 Years After Sentai team, they'd have to obtain the Graphite, Talon, Aqua, Purple, and Silver Rangers powers, use them, and then replace them with their original powers again, or something to that effect. Just because they have the same color powers as the Future Kyoryuger's secondary powers doesn't make them counterparts.
But what if Dino Super Charge covers the 100 Years After story and there are full fledged counterpars of the Future Kyoryugers? Would they still be counterparts of the main team? Besides the fact they use the main team's powers at the end, nothing about the two teams are similar to each other.
EDIT: I can see what you mean on both ends, it just feels like a stretch to call them counterparts in that there may be real counterparts later. Although there are a few cases of that around the wiki, so it may be pretty harmless.