I took a minute to reclaim my bench space in the garage! So much better working off a proper bench! Enclosure is looking super sleek, i am stoked with it!
Drilled all the holes through the deck and then counterbored them with a spade bit for the t-nuts
I tried clamping them in and while this did work, it tended to follow the curvature of the deck, rather than following the line of the hole… this resulted in some of the screws cross threading when I tried to install the enclosure 
The problematic nuts were removed and replaced. If i ever do this again, I will skip the clamp idea and just go straight for bolting them in. The bolts pulled the t-nuts in beautifully.
I still don’t have the basalt fabric I ordered, so I think the next step is to position the bindings and install t-nuts for them as well as for the top box.
I also need to countersink all of the aluminium holes to appease @Bavioze … i wasn’t going to do it, but I tried a few and it looks great.
I haven’t actually designed anything to interface the deck and the top box, so I’m gonna need to find some CAD time!