Hello Frank -

> Not really, but it illustrates my point very nicely.  If I put a feeder box
> (flat bottomed) on top of such a super, I would fear crushing the bees on
> top of the frames, (Only 1/8" clearance

This is correct, crushed bees with flat bottom items on top. However, most
inner covers are designed with the panel set into the middle of the
perimeter framework, giving you the other 1/4" you need above the frames.
Same thing with feeder boxes, the one on my site allows for this and has a
1/4" lip around the bottom edge. You can always increase the space pretty
easily with strips of wood, plus, bees will tend to build comb in an
oversized space more than they will an undersized space.

> three sides (The usual design from what I have seen, and the one shown in
> the Langstroth plans) will leave a 5/8" space beneath the bottom most
> frames, and the bees will likely build burr comb in this space (mine do),

Yes, they may tend to build a bit of comb below the bottom bar but I
personally have never found it to be a problem. If they want comb there,
then let them have it. They know better on the ventilation needs they have.

In regards to Dave Cushman's point about the frame and super dimensions
being off an 1/8", I should mention that the design on the plans do not
allow the side bars to be flush to the top of the top bar, but instead are
below the top bar by 1/16" so there is no risk of hitting the side bar ends
when one goes to scrape the top bar clean with a hive tool. I'm pretty sure
the other 1/16" is accounted for somewhere else but I'll have to look it
over again to be sure.

Regards,
Barry