I can't comment fully because I don't have a Roadster and the original Cooperman pics don't show the whole intake path. The V6 mustang is a better photo in that respect so if anyone has that perspective from the same model Roadster it would be nice to get that posted here.
However, IMHO what Cooperman has done will not spoil the tuning of the system because it's all on the dirty side of the intake and he has not altered the clean side at all.
By the time the resonance gets through the filter it's strength is gone anyway and as I say, from what I can see, there are no changes between the ports and the filter.
The dirty side of the airbox is there predominantly to make the system quieter and collect cool air.
I'd be interested to see where the throttle body is in the Roadster intake system.
I can’t profess to be an expert on this, but I agree that air boxes were originally introduced simply to diminish the induction noise. However, it was then taken a step further by mathematical design, to achieve resonance in the mid range, where torque may typically drop off due to valve overlap on modern engines. Resonant design means that air flow through the box is at a maximum, with little restriction. So that is all happening and remains happening within that particular rev range, on the dirty side, allowing maximum air flow in through the filter to engine. Any large holes cut in the box are bound to upset the point at which resonance occurs and could poorly affect torque where it is most needed. Possibly, what MMC have done by chopping a hole in the bottom is not very scientific but can’t help feeling that even more holes will destroy any resonant capabilities that may have existed. The argument is easily settled of course by taking it for a thrash but to be more certain, by a dyno-test of before and after.