I think the idea is to set the neck jig to the amount of bow you want in the neck, then once it's strung up you adjust the truss rod for that much bow.
Nah man,...sounds kinda like a dog chasing his tail.

(...Sorry,

that wasnt cool.)
I should have explained it better,
It took me a while to wrap my head around it also but I think I understand it now.
The whole idea of the jig is to be able to recreate the effects of string tension.... with the strings off.
When you surface the frets you not only want to have the neck flat....but flat, as if with string tension.
So you say, ***? ....flat is flat! Right? No
Ok...here is as close as I can come to justification of this jig...
So when you straighten the neck with the truss rod, with the strings OFF.... the entire neck is flat.
When you straighten the neck with the truss rod, wth the strings ON... the neck is flat, for the most part, but flexes forward slightly, ...except for the "heel" end attached to the body, where the last few frets are. Hence the illusive "ski jump"
You want to recreate the same conditions created by string tension.
You can do that fairly accuratly with the jig by not only supporting the neck in the same place, but also pushing forward on the top of the headstock, whilst pulling back just above the nut with the strap.
So that is why,... since I am choosing to dress the frets before I'm able to put strings on... (for easier access ).... I sanded a bit of fall away into the last few frets ...in anticipation of most of the neck flexing forward, but staying put where it gets thick. (At the heel, by the body)
Hope I made some sense of it there

@Gilmourisgod