If you take some fine sandpaper and carefully sand down each end of the "offending" templates, they will eventually match your cardboard ones. Seriously though, it shouldn't make much of a difference if both players use the same set of templates, no one gains any advantage or disadvantage. If I was playing someone quibbling over something so trivial, I would just pack up and go home. I play to have fun and when someone starts to suck the fun out of a game, I go play something else.
I don't think people are worried about friendly games with respect to this.
I've played a lot of miniature games that use measurement and find players get very good at knowing almost exactly where something will end up. Switching templates on them (one way or the other) that are different could end up meaning the difference between hitting an asteroid or not, running into an enemy, or not, and while I don't have an exact percentage difference here, my one-turn looks like enough of a difference that it could throw off myself or my opponent to use each others' templates.
There's the fact that when you pay a premium price for something you'd expect it to be as precise as possible (and maybe it is, just to a different printing of FFG templates). I probably should checked more closely before getting multiple sets or at least figured out their standard before doing so.
All that said, while I think the difference is enough to throw a player off who is used to a certain set, there's probably not a big enough difference for it to be significant advantage or disadvantage in this game. Still, I'd like to know the issue and all it takes is for one person to make a stink at an event to ruin the fun, and you can't just pack up your set and go home there . And really, it would be fine to switch in that situation, but it would be a bummer to not be able to use the templates I purchased and think look pretty sweet.