The ATjr I mentioned, which could stand to generate some excitement in this thread if nowhere else (ok I'm getting excited if no one else!), is in reality just an xt in virtually all respects. That and a fugazzi.
My impression, which admittedly may be fuzzy because I was only a teenager at the time, was "ATjr" was sort of an informal name for the first crop of "Baby AT" cases. Which, as you say, were essentially just slightly taller XT cases that had a top that was styled more like an AT. (IE, the drive positions were only exposed on the far right, the "middle" bays were hidden.) It was a little later that the fully XT-derived ATjr morphed into "Baby AT" in the sense of the diverse family of mini/mid-tower cases and small desktops we had up until ATX took over in the later 90's.
The first "AT" my family owned lived in an "ATjr" case, the result of an attempt at upgrading our PC/XT clone going pear-shaped because the 286 motherboard we mail ordered ended up having a component just barely too tall to fit under the drive bays. That resulted in a run to the local computer store to buy *just* the "AT Junior" case, which in addition to the styling changes had the maybe 1/2" of additional clearance under the drive bay needed; didn't even get a power supply, an XT power supply would fit those cases so I used the one we had. (A "real" AT power supply is of course taller and has an "L"-shaped indent to fit around the wider motherboard.)
(I would have taken a hacksaw to the XT case to solve the height interference problem except then our full-height hard disk no longer would have fit along with two floppy drives.)
Apparently some people did advertise computers under the "ATjr" name. In this case, ironically enough, an XT class machine. If they advertised them as such I suppose they must have also slapped labels with that name on them. (The case I bought back then was blank, of course, so the computer store could slap their own badge on it):
But an xt in a baby AT case, really unrelated to this discussion totally.
Why? If we're talking about making a motherboard for people to play with it might be useful if it fits as many cases as reasonably possible. (Unless, yeah, it's specifically about making a
reproduction motherboard. There was someone selling a reproduction 5150 motherboard a few years ago, in the vein of those Apple II reproduction boards; you can probably count the number of clone cases with the 5150's slot spacing on one hand, so if the goal is to do the same for the 5160 then by all means copy that exactly.)
Basically the dimensions that really matter are the slot spacing, the distance between the slots and the back, the position of the keyboard connector relative to the slots, and the relative positioning of at least *some* of the mounting holes to those landmarks. After that as long as you're in the ballpark you'll probably be fine in terms of gross dimensions; if you make the board the same size as a 5160's that's probably the safest bet because it's *slightly* on the small side as full size "Baby AT" motherboards go. The only thing I'd suggest, again, is looking at adding some of those extra holes. There are high-res photos of 5160 and 5170 motherboards out there, if you can find some that are sufficiently dead-on that you can overlay them just chart any differences between the hole locations, put holes that match both into your design, and that will probably be good enough.
(You can probably get pretty good measurements from those photos if you're sneaky and, again, you can find a dead-on view. Remember, the pin pitch in the slots and most of the DIP chips is going to be ten pins to the inch. Use that to calibrate a ruler to the photo and go to town.)