Well, I have had to replace the sights on a P99 before. The front sight is easy - if U are gonna put night sights on that - there is only 1 way to do the front sight.
As for the rear sight - I don't know about your P99, but both my fullsize and compact P99s have the rear sight slightly off center. Just take a long hard look at that. Then, when U put the new rear sight one, place it the same way.
I understand what U are saying about the boresighter, and that U could use it later. But quite often they are not perfect anyway. They tend to be a few inches off sometimes - the purpose of the boresighter is to get you on the paper to start off with. THEN you make fine adjustments from there.
When I used a laser to sight my PS90 in at 50 yards w/ my eotech, it was 4 inches high at 10 o'clock. But, it got me started, and I took it from there. It would have taken me forever just to hit the paper on my own.
But - at 7 yards, U will probably spend more time messing with the boresighter than if ya just did it the other way.
Just my suggestion.