I know a lot of people have cut them shorter without any issues, but if it were me I'd leave it alone. I believe those poles extend that far down to add more ridgidity to the tub sides when slamming the door closed. There's a second baffle and a bolt further down in the door jamb (below the catch) that holds the poles in position, this gives two points of contact to hold the B-pillar in alignment and act as a solid piece. If you cut the poles shorter, there're really nothing to prevent them from flexing right at the joint. The bolts on the flange are more than enough to hold the hardtop down, but they do nothing to hold the hardtop on the same plane as the tub side.
I think on mine, the problem is exacerbated because of the thicker door weatherstripping, when I push on the door near the latch, I can see the sides bowing inward slightly due to the pressure. If i didn't have those poles going all the way down into the jamb, I think I'd probably have a lot more deflection and have a harder time getting my doors to latch completely.
Just my $.02
