Take a deep breath and stop thinking so hard about windscreens. The short answer is, forget about flashing, use oven liner, forget about holes, just notch the bottom edge of the windscreen.
The long answer is:
MSR windscreens are made of soft aluminum of the same gauge as oven liner. Either the MSR windscreens or homemade ones of oven liner or cooky sheet will last for months of continuous use and years for most of us. That's enough durability.
Oven liners and cookie sheets feel crinklier than the MSR windscreens because they are impact hardened during the manufacturing process. You can soften them by heating and quenching. The process is called annealing. In a darkened room, heat the aluminum until you see the first florescence - the dim red-brown called 'cherry red'. Immediately quench it in cold water. If you get it too hot, it will burn through. That will let in too much wind.
Flashing windscreens are heavy enough to serve as pot supports. If you are not going to use the windscreen to support a pound or more of water, there is no need to use flashing.
The reason flashing browns is that it has a thin coat of varnish. Fumes from the burning varnish are highly toxic, so sand the varnish off before using the flashing.
RE: warping. If you are not making a flashing pot support/windscreen, this will be irrelevant. But the annealing process described above will prevent warping. You can use the varnish as a heat indicator -- with good ventillation -- and quench the flashing as soon as the varnish moves from light brown to a blacker brown. After quenching, sand the varnish off completely. It is easy to see after you char it. The reason for doing all this is that new flashing is impact hardened just like oven liner. That means it has lots of built-in stresses. Uneven heating releases these stresses unevenly - so the piece deforms. Annealing releaves the stresses.
Vent holes: Don't waste your time with holes. Just cut notches around the bottom of the windscreen. They will move more air; they will shield the burner better; they will not weaken the windscreen; they will let the screen fold or roll up easier; they are easier and cheaper to make. You can spend a lot of time, money and effort on vent holes with minimal benefit. In the first place, they only work well with flashing - because it is so thick. You could punch vent holes in oven liner, but then it won't fold or roll up well.
Holes must be large enough to overcome the boundary layer effect. The first 1/16 of an inch inside the circumference of the hole is dead air. In other words, a hole less than 1/8 inch in diameter will not pass much air except under pressure. It doesn't take much pressure to move air through the hole, but a bigger hole will be much more efficient. It's a sliding scale sort of thing. 1/4 inch is about minimum. Now then, drilling a hole 1/4 inch or larger in flashing is hard enough. It is just about impossible with lighter material. You can punch it, if you can find a punch big enough. Why bother? Just notch the bottom.
If you notch the bottom, the concern over which side to put the holes in becomes a non issue. The notches are on the ground where friction against the ground reduces the effect of the vagrant zephers. There may be rare conditions where the wind creates a problem, for example, if the stove is set up on a rounded boulder that entrains the airflow along its surface. Then a few strategically located pebbles - or just moving the stove (duh)- will take care of the problem.