Hi C_K,
You get to answer your own question here. I agree that Dave's drawing isn't too clear on the dimensioning of the rebated top rail dimensions.
The apex of the runners (plastic or metal) sit 6mm above the horizontal on the rebated rail and the top of the end board.where the frame top bar sits. So thats runner 6mm + top bar thickness 9mm = 15mm. OK, so that's that dimension sorted, but hasn't answered your question yet.
If your frame lug rests on the 30mm flat, giving you 8mm bee space between the frame side and the box side wall it poses two problems.
1. How will you be able to get the hook of your J-type hive tool between the top of the rebate/end wall and the lower surface of the lug?
2. Having worked out that it would be impossible as soon as you built it without rails, how much more impossible one the bees managed to propolise that lug to the rail?
So you have now worked out your own answer? The rail gives you jacking space and bee space where they will scuttle out of the way of your hive tool as you jack up the lug to remove the frame. The apex of the triangular runner gives a point contact on the lower surface of the top bar and bee space either side of it, giving minimum opportunity for getting glued up. You won't believe me when you are prising frames out of a busy hive, but consider how much worse it could be if you didn't use runners at all.
The critical dimensions are all determined by the frame sizes (which you will find on Dave Cushman's site), bee space and either 1 or 2mm clearance for the ends of the frame top bars.
Bearing in mind that the difference between a standard deep and a super is the depth,
see this drawing. Looking at the diagram top-right, I see no reason why the dimensions should not allow the bottom of the top rail rebate and the top of the end wall should not be flush. Likewise the bottom rail and the end wall bottom. Just maintain proper bee space. The bottom rail is splayed/beveled so as not to retain rain.
Happy building. Make sure you understand all the dimensions before accepting them as gospel. Just remember that bee space is 7.5mm +/- 1.5mm. That explains my anomaly with 8mm between frame sides and box sides. 1mm clearance on the ends of each lug means that space could vary between 7mm and 9mm with a bit of float on the frame taken into consideration.
I hope this has been of help to you. If you were to make a Nuc with 12mm ply, then the width of the rebates in the end rails would need to be increased accordingly.