If it was a 3/8", I'd be concerned as well. But it's 9/16" and this nailer was made specifically for engineered; even the cleats are different. I'm not using the mallet to tap the boards together. I have an old Award longstrip tapping block that works great. I just slam it into the tongue and the boards go together; rarely need to use a hammer or mallet with the block. If I had a Spot Nailer, I'd have used that but I already own eight pneumatic nailers. You think that's enough? Here's the list:
(2) Senco finish nailers
(2) Bostitch M111 FS staplers
(1) Porter Cable brad nailer
(1) Power Nail Model 200 cleat nailer
(1) Porter Cable framing nailer
(1) Senco multi-purpose/underlayment stapler
Anyway, on the Power Nail 200, the shoe/boot affair only contacts the tongue and the face of the board; never the edge. So no worry about damaging that unless you set it down wrong. And you only hit it lightly; no need to whack the crap out of it. The boards are already together. After laying about 300 ft, I've got two small spots where there is board rub and a squeek. A slight deflection. Not sure what's up with that yet. I may need to pull a few boards. Perhaps the nailer misfired and didn't install a cleat. Or the cleat went in too far. Or a low spot I missed in the subfloor? Who knows? I'll need to investigate. I hate when that happens!