A lot of the infamous $45 extra charges for simply seem to be for unusual requests. I suppose Tele pickups just aren't as commonly asked for as Strat pickups.
Frankly, some of the things Warmoth charge extra for boggle the mind (apparently getting a Tele routed for a left handed bridge, i.e. reverse angled pickup, is a $45 extra), but it's so convenient I almost don't care. E.g. USACG do any neck back contour and fretboard radius you want at no extra charge, but ordering from them means an international call at a crazy time at night for me. Warmoth let me just click, click and checkout and I'm done. That's worth the extra cost alone, to me.
Of course the missus doesn't appreciate me chalking up all the Warmoth extra charges, but well... she said I didn't need a 17th guitar either, so what does she know? :laughing7: