I'm looking for an exact clone of the US military issue M9A1 sidearm for the collection, but I am not sure if there are differences between the M9A1 (not the M9) military vs. civilian version. I haven't had much luck finding a good comparison post online so figured I'd ask. Anyone know the details (from design changes to the markings)?

I am not an expert, but as best I know, the difference is just in the serial number and markings (the M9a1 Commercial has civilian markings and that unsightly lawyer stamp unlike the M9 Commercial).

One takes glock mags

Dick.

Function nothing really.

I can't say for sure since I've never seen one in person. But at least some that were used appear to be straight off the shelf M9A1 guns. Stupid warning marks, "92FS" on the slide and all. Granted these may have been (early) demo guns or something.

Here. Looks like writing on the dustcover:
http://www.ar15.com/mobile/topic.html?b=5&f=15&t=150057

http://www.mcipac.marines.mil/News-Center/News-Article-Display/Article/532250/new-pistol-brings-new-capabilities/
https://commons.wikimedia.org/wiki/File:U._S._Marine_Master_Sgt._Michael_E._Schellenbach_places_his_M9A1_pistol_in_a_weapon_stand_at_a_pistol_range_at_Marine_Corps_Base_Camp_Hansen,_Okinawa,_JP_July_26,_2013_130726-M-AQ282-452.jpg
(Click on pic for blownup view).

https://upload.wikimedia.org/wikipedia/commons/9/91/U._S._Marine_Master_Sgt._Michael_E._Schellenbach_places_his_M9A1_pistol_in_a_weapon_stand_at_a_pistol_range_at_Marine_Corps_Base_Camp_Hansen%2C_Okinawa%2C_JP_July_26%2C_2013_130726-M-AQ282-452.jpg

The handful that I've seen in person were identical to the one sold to the public, down to the lawyer warnings. As I understand it, the M9A1 is an all "off-the-shelf" weapon.

M9A1 mil and civilian are all of the same production line iirc. There should be zero differences.

My A1 has the rounded trigger guard, I have seen many with the squared version.

That's a 92A1