It looks like you guys are asking two separate questions, so I’ll answer each….
1. The 1.5″ overhang of the countertop is deliberate. It gives you a slight overhang and more counter space. It’s also more comfortable when you have a sort of toe space between the two edges, take a look at your kitchen counters, there is a 3.5″ toe space on most cabinets. This should not cause and problems trimming the face, just run a 1×2 or 1×4 all the way across the top of the lower cabinet opening the trim down at the verticals with a 1×4. If you decide to put doors on, the face would then be flush. Face trim or doors are not required on the bartender side, but it’s your option.
2. on page 18 & 19, there is a gap of 1.5″ where parts 61, 62, 63, 68 and 69 meet the side upright supports. This 1.5″ gap allows for the 1.5″ thickness of parts 70, 71, 72 to meet flush at the top. I don’t see too much confusion in the drawing. When done properly, the edges of parts 61,62,63, 68 and 69 should be flush at the top with parts 70, 71 and 72.
(Notice on page 18 it says to cut the trim but don’t secure yet, that is to allow you to make it flush to the real (70, 71, 72) parts. There is even a note that points out the 1.5″ gap.)
dvw – tell your wife she’s a natural woodworker and mechanical engineer! 😉
Cheers!