I'm picking up an AT1-C tomorrow (because I don't have enough bikes already ) and looking at the photos it also has the "later" design without the separate mounting plates, but still has the side mounting exhaust.
I would think Mark's theory is a good one and it's probably a phase change as they moved towards the later design.

You can never have too many bikes, Pete! 

I look forward to reading your new shed build thread, to go alongside Mako's!

All the parts sites show in their exploded views a #261 frame with a bracket for the key switch on the left front downtube and no slotted bracket has been welded on the top of the frame for the seat prop rod. This makes perfect sense for the 1969-70 AT1/CT1 series. However, 1971 models should not have the front bracket, but they need the seat prop bracket. The exploded views of the #315 frame for the AT2/CT2 models shows the correct welded brackets for 1971 models. As discussed here, the #315 frame does not show the triangular rear engine mount brackets. My 1971 AT1 has no bracket in front and does have the seat bracket and the engine mount brackets.
Are the AT1/CT1 and AT2/CT2 engines interchangeable with the # 261 and #315 frames or not? If not, is there some missing interim model frame for the 1971 models that is not shown?

 

1960Super10, parts diagrams are not "technical drawings" by any stretch of the imagination and they certainly did not show every detail.  Some drawings barely resemble the actual part or are wrong/misleading.   The diagrams are often not good enough to use for "assembly" either.  They are simply parts diagrams with a general representation of the part and (usually) the approximate location on the bike.

The AT/CT engine case mounting points are identical from 1969 to 1973 if that's what you're asking?