Wow. I've downloaded three versions now and the sizes are nothing like that different.
12/20/2015 04:39 PM 28,716,961 ATBA164DOM (revised 20151218).pdf
12/17/2015 06:51 PM 29,007,260 ATBA164DOM (revised 20151120).pdf
11/13/2015 06:54 PM 28,714,946 ATBA164DOM.pdf
line on the bottom of the first page of those read, respectively,
00X31-TBA-6002 2016 Civic Sedan Owner's Manual - Ver. 3 AOM03021
00X31-TBA-6000 2016 Civic Sedan Owner's Manual AOM02073
00X31-TBA-6001 2016 Civic Sedan Owner's Manaul - Ver. 2 AOM02710
I agree that it seems weird that the 2073 and 2710 manuals seem out of sequence. But that's what I see.
I don't have the full version of Adobe Acrobat to compare them, but I saved them as text and used Word to compare them. Differences are very minor and many are not substantive. In one change, they changed the color of an indicator they were referring to. That kind of stuff.
They also have the separate Navi manual and the Owner's Guide (it didn't used to be there at all):
11/13/2015 06:49 PM 6,843,006 ATBA1616NV.pdf
12/17/2015 06:44 PM 24,113,046 ATBA1616OG.pdf
00X31-TBS-8000 2016 Civic Navigation Manual AMV02168
00X31-TBA-G000 2016 Honda Civic Sedan Owner’s Guide AOG02171 31TBAG00