I haven't used a high build poly on a surface like this - so I'm just extrapolating here.
How big/deep are these nail holes and divits? In general, poly isn't something you'll want to pour into a large defect to fill it in. With regular poly, on porous woods like oak I use a pore filler prior to applying the finish or the pores telegraph through the finish. I've heard of folks using an epoxy to fill in large defects under a finish.
In cases like this, a test board is invaluable. Mar it up - add dings, holes, etc like you have on the door. Then try applying your poly straight and see if you are happy with the result. If not, try epoxies or similar techniques until you get something you are happy with. Easier to experiment up front than try and fix it afterwards.
Measure with a micrometer, mark with chalk, cut with an axe.