I don't know if anyone is still looking on this thread, but
I have a three button bag--I wanted it for my SPN cosplay (full album here:
http://imgur.com/a/amMMW ) and did a ton of research. I ended up contacting Canadian military surplus and found out from them that
the SPN prop department made the three button bags by cutting down five button bags. I cross-referenced this with the show, and sure enough, you can tell:
-The end with the plastic piece (for nametags) changes from side to side (sometimes it's on the end that the zipper opens, sometimes it's on the opposite end): the prop department had to take off the ends of the bags when cutting them down, and sometimes put them back on the wrong side
-The fabric covering the end of the zipper (where it connects to the fabric seam) is sometimes there, sometimes not: When cutting down the bag, you would want to avoid taking off the webbing strap (because it's a pain to sew). Instead, you cut out the extra fabric from the ends and from the middle (where the fabric attaches to the zipper). This has the added bonus of allowing you to cut out where people commonly write their last names on the bag (commonly written right below the zipper--you can cut this part off).
-I "measured" the on-screen bag using proportions we know, and found that, sure enough, the proportions between the buttons on the three button bag are the same as on the five button bag--meaning the prop department just cut off the two end buttons (one from each side) and left the three middle buttons.
You can tell other slight differences with the different prop bags they use on the show--these slight differences mark ways that the prop department varied in their reconstruction of the three button bag (from the five button bag), and therefore how they actually made the three button bag.
I hope this helps anyone who is still looking for the three button bag!
Long story short: My belief is that the three button bag was never produced commercially, hence why it's so "rare." However, you can make your own from the five button bag.
Have fun!