Try this test. Insert one of your P99 mags into your PPQ M2. What you'll find is the button latch on the PPQ will latch into the P99 latch hole....leaving the mag about 1/2" from being fully inserted. Now, can you add an PPQ M2 latch hole below the P99 hole? Sure you can, but every time you insert a P99 mag into your PPQ M2, its going to latch into the first hole it comes to....which the P99 latch hole. Now, you could push the mag release button in and THEN give that mag a final push and it'll click into your newly made PPQ M2 latch hole.
So, it'll work...just not the way you'd prefer.
If you want to have a mag that'll work in both PPQ M1, PPQ M2 and P99, you'll need to start with a PPQ M2 mag. THESE mags can be modified with the addition of a PPQM1/P99 latch hole. AND, when done correctly, and you keep the hole small enough to work, meaning NOT as large as the factory hole, you'll wind up with a mag that will slide in and click in to all three platforms. However, if you make that hole just an rch too big, it'll hang up, stick or even latch into that newly added hole.
Here's a sampling. On the right is a Beretta 30 round mag, with an added M2 and M1 (red circle) latch hole. Second from right is a Sig P226 20 round mag with an added M1 hole (red circle) and the standard Sig latch hole opened up to accept the larger PPQ latch bar. Third from right is a PPQ M2 mag with an added M1 latch hole (red circle). On the left is a P99C 10 round mag with a modded +2 base plate.
All of these work perfectly in either platform. But, the newly added M1/P99 latch hole size/location is absolutely critical.