So I've been using Whisperlites for years mostly for work, and was always trained to 'catch' the flame as the priming flame was going out (wait until the priming fire is almost out and slowly open the valve 'catch' the flame and lighting the stove)
But a company I just started working for teaches to let the priming flame go out, then open the valve until you hear the gas and light the stove then.
Do you all know any pro's or con's to this method? Does it really matter how you light it?

The MSR manual says,

"1. Wait for preheat flame to reduce in size (approximately 2 minutes).
If flame goes out, wait 5 minutes for stove to cool before relighting.
2. Open Pump Control Valve 1/2 turn and wait for steady blue flame.
3. Slowly open Pump Control Valve."

So you've been doing it the way they suggest. If you wait for the preheat flame to go out, there's a chance it will cool off too much before you get it lit.

I've had them flare up pretty good, trying to light them after going out. That's the real reason for lighting them the way you do . If your bottle is well pressurized you can trim some facial hair. By the time you hear a loud enough hiss to let you know gas is coming out, a little cloud has formed above the burner. Poof.

With my students I try to get them to light the stove as directed in the manual but they usually can't seem to time the flame going out to actually getting the stove lit. Most of them end up getting frustrated and wait for it to go out on it's own and then quickly opening the valve and lighting it. So far we've all been safe but I can see where not doing this quickly could end up in a disaster of sorts.

That's all for now. Take care and until next time...be well.

snapper