Will those solder joints then be mechanically strong enough to stand up to shield removal and reinsertions over time?
I think so. since you have control over how much solder is in the initial puddle, you can use as much as you normally would. this puts the header a little farther away from the board, but you would presumably be doing this with all the other headers as well.
The approach I use in this situation is to push the pins so that they are flush against the plastic piece of the header. Then push the header through the board from the opposite side, so the plastic is on the non-copper side of the board and the pins are long enough to be useful and still be soldered.
I think it might work best to push them through then solder then then bend them as I described, in that order.
I still do not know why they chose the spacing that they did.