Avatty,
I wouldn't say the manual is incorrect, but I can tell you what I did and I'm very happy (you might say proud) of the way my canopy turned out.
Yes, I left a 1/32 overhang on the rear window with respect to the shim on the roll-bar. As you've probably figured out, by the time the shim is deburred, countersunk, and riveted there can be some very tiny deviations from it being perfectly straight/aligned with the roll bar gap. On the other hand, it's relatively easy to get the rear window perfectly aligned with the canopy itself. Leaving a 1/32 overhang hides these deviations and allows an easier time "setting the gap" between the rear window and the canopy.
Page 38-21 calls for a 1/32 gap in Figure 3 while Scott in post #2 recommends a 1/16 gap. I began "working" the gap toward 1/16" and decided that a .050 gap looks about right for my taste. If it needs more gap, I can easily take a couple of hours and increase the gap while the canopy is on the plane.
For me, the bigger challenge was that once complete, the rear widow and the canopy weren't perfectly flush. There were a few places where the rear window or the canopy was .001 - .004 high/low. This doesn't sound like much, but when I saw the profile on a glossy surface, I thought it needed some attention.
When at Oshkosh, I looked at this on a number of RV's and found that many (most) of the pop-up canopies tend not to fit perfectly flush to the rear window. I estimated some to be as much as .020 high/low. I made a number of shims (washers) out of "feeler gauges" and placed them at 6 places between the canopy or rear window and the frame/roll-bar. The canopy is now perfectly flush with the rear window.
While you have to look pretty hard to see this on many planes...it's there. My fear was wind noise, drag, potential damage....and loss of pride. So I felt the need to make fit and finish better.