For mounting my supported rails I clamped them in place accurately, then used a centre punch to very lightly mark the centre as a best guess. You can't see if it is central until you remove it, so I then looked straight down the hole, and made subtle adjustments with the punch to 'push' the hole around a bit. When happy I gave it a big hit ensuring that the punch was very vertical. Then double checked it and moved on. Finished by drilling the pilot and tapping the hole. Took along time but when it's done it's done.

In terms of thread engagement I've always used up to 1.5D as maximum depth as you get rapidly diminishing returns in terms of thread load for the deepest threads. So M8 has about 12mm of thread. Not detrimental to go over, but not helping either.

In terms of minimum engagement I must admit that I've always used judgement, but out of interest I had a look at Roy's site (DIYCNC) and found the following. Lots of maths to get stuck into but the upshot in minimum thread length appears to be:
M3 = 2.4mm
M5 = 4.0mm
M8 = 6.5mm
These are for bolts and holes of the same material. Steel bolts into aluminium holes are supposed to be deeper.

Link : Screw thread Calculations

Scroll right to the bottom and find the row 'Length of thread' and the symbol Le. There's an approximate calc, and a more accurate calc.