The matte box doesn’t get in the way of a mounted shotgun mic, even when the flag is up and the mic is wearing a rabbit. I’m using a Sennheiser ECM-60. However the mic appeared in frame at the widest zoom setting. I solved this with a Rycote camera clamp adaptor (CCA) which raises the mic a bit but which also adds an essential extra level of noise insulation – the camera mic mount transmits too much noise.
As far as handheld work goes, it’s a slightly cumbersome configuration and requires two hand support unless you have particularly strong forearms. This is the other reason I’m thinking of using rails instead of the lens mount for the Petroff matte box – it means I can also support the camera with my left hand under the rails and still reach the lens controls.
However I’m also wondering about the value of one of those shoulder mount adaptors for ‘palm-held’ cameras. The camera performs so well it’s worth doing some experimentation to get the handheld side of things worked out.