The SPEC boot should not have holes in it. The holes punch out for use as a trim boot only. The whole point (no pun intended) of the boot is to contain grease, it wouldn't make much sense to put holes in it.
To pack the chamber, I use the syringe applicator to pack around the spring, making sure to completely fill the area between the spring and the piston shaft. Then I put a bead around the bottom of the chamber on the HP o-ring end, basically filling that cavity except leaving a channel for the bullet/piston shaft to go through. Then when you start threading the body together, lots of grease comes out the holes. If you're really clean and really cheap you could capture that grease to re-use. Since I want to be sure that there are no air pockets, I err on the side of extra grease and a lot comes out the ambient chamber.
If you're using air only, silicone grease is much thicker and it lasts forever. The tribolube 66 is thicker than the 72 (I can never remember those numbers) and a little cheaper, so that's what I use. In my packed MK5 I'll probably go to silicone and just use that first stage with air.