Oh great, thanks a lot for the explanation Sengoku Strider. Everything makes perfect sense now.
I can confirm that the spine cards on the limited (cardboard case) versions say the same thing than on the jewel case versions pictured here. Which makes sense since you say they were released at the same time, and they give access to the same bunch of goodies.
So it seems that here we simply see an exemple of Sega printing way way more limited version (cardboard) than standard version (jewel case).
Madroms and I confirm that, contrarily to what is stated on Sega Retro, the volume 3 exists in jewel case. He found his on ebay (pictured above), and I found mine on a forum (no spine, pictured below as spoiler with the whole jewel case family).
As for why volume 3 is rarer than 1 and 2 let's guess it is because the sales were not as high as expected when the game came out one by one and they decided to lower the standard version print number.
Bravo jolie Ln, tu as trouvé : l'armée de l'air c'est là où on peut te tenir par la main.