When one side is saying "don't just crank up the boost without doing x,y,z" and the other side is saying "nuh uh, it's totally cool, just crank it up" I would say yes, the uninformed side should keep their mouths shut, because when people act like they know what they're talking about, but don't, less informed people take their advice and blow s*** up. To be frank and direct, running additional boost without properly modding and tuning for it is a bad idea. Period.
Whether or not the motor can take it, whether or not some people have had success doing it, is irrelevant until the leg work to *prove* it's safe is done. No one on here talking about how great their motors run with extra boost have provided AFRs, EGTs, dyno plots, etc to demonstrate the MS3 motor is just fine with more boost, and until that's done I wouldn't recommend that anyone not willing to destroy their motor do anything to it. And if you're going to do it anyway, have a heart to those that might not know what they're getting into when you talk about what you've done and make sure to emphasize the risk you're taking.
The fact that Cobb's base maps for the AP don't make more power over stock tells me they're seeing things on the dyno that indicates the motor is already making what it's gonna make on the stock turbo/fuel system. If it were safe, I'd expect Cobb to release maps that bump power on a mechanically stock MS3 like they do on the WRX/STi. Maybe they haven't gotten there yet with their tuning, but until I see the proof it's safe, I warn folks of the potential risk to modding irresponsibly.
And as far as blowing the car up with a boost controller and going back to Mazda for a new motor under warranty... well that's the lowest of the low. That's basically stealing from Mazda, which eventually makes it a million times harder for those that actually have warranty problems to get them taken care of by the dealer. Hell, the whole reason the Mazdaspeed intake got stop-saled may have well been from a few performance minded people that had them going and running their cars lean with additional boost and falsely pointing the finger at the intake. So now everyone that wanted a warrantied intake suffers.
All I'm saying is, for the good of the online community, people should do their best to make statements with full disclosure, and take personal responsibility for what they're talking about.