If you run #16 or larger wires under your track base, you shouldn't have any heat issues from the wires. If those wires get hot, you're feeding them with a LOT of current. You're far more likely to generate heat where the wires connect to the track or at other connection points that can have resistance.
In any case, make sure you have good circuit protection at the transformer feeding the wiring to insure any shorts will interrupt the current and not create excessive heat.
