I'm honest and fair I'll admit:

snipe

Rearranged, I'm of no use to trains:

spine

Again, and I'm an overt place, warm and well-lit:

penis

I'm honest and fair I'll admit:

Snipe, a bird perhaps capable of deception. We'll have to cover our bases with truths and lies to be sure.

Rearranged, I'm of no use to trains:

Spine (useless to trains)
or
Pines (a lie! Pine is a type of wood which could be used in railroad ties)

Again, and I'm an overt place, warm and well-lit:

Penis (Warm, though often illegal to be overt and well-lit)
or
Peins, Netherlands (a lie! With moderate/cool yearly averages and a population of just 270 (in 2006), Peins is likely secluded, cool, and poorly lit.)