I rekon you will be ok, just WATCH them like a hawk when they do it. The best hour you will spend making sure you save hours later if you have to sort issues when it's too late.
The main one imho would be to put a mark on the top windscreen rubber where the glass edge rubber runs onto the roof cross-member rubber (some chalk maybe)
Do the same at the bottom too once the plastic covers come off.
The screen should fit square and nice top and bottom. It seems to be the fitting too low down in the aperture that causes problems as it then has too much gap at the sides.
If you can find something appropriate, those polycarbonate 'wedges' the right size are probably a good bet. I saw BMW using these on the Megafactories to set the windscreen location, the gap should be the same size and tight both left and right sides near the bottom and top of the A pillar.
Find the right sized wedge and check it before to make sure you know how it should be!
As said though, it should be fine, but I would watch them! Brand of glass also is not an issue as long as it's someone good like Pilkington etc, the screens can actually be better made than BMW ones (due to more modern process/standard since the screens were originally made)
Dave