My initial thought is that it is not, that the ley lines weave in and out between the planes, only intersecting at random points (thus keeping the lines rare and valuable).
I run things by the 'yes, and ... / no, but ...' method of GMing, so it seems you just need another plot thread for them to follow up on when they find out that ley lines do not fill the center of the earth.
Maybe you build an adventure for them to explore the center of the earth and through a mysterious event they end up elsewhere where ley lines do converge. Maybe they find a way to scry through solid earth and find a lost civilization beneath the darklands -- or its ruins. Maybe they find that a secret cabal already has the answers and is bent on making sure the party never learns the truth.
Also, their vision of ley lines sounds like some great chances for a Final Fantasy VII crossover. If it is coming from that, you might want to steal a moment or two from that game just for laughs.