You won't hear Hideo Kojima talk about it in a Kenji Eno documentary. It's the kind of game Eno seemed to hate making, one with licensed characters. But...he made it; you can look at the credits yourself below. (Spoiler: He's credited as the game designer.)
SD Gundam Sangokushi Rainbow Tairiku Senki is an arcade run and gun developed for Banpresto by Kenji Eno's company EIM (as confirmed by the game's director, Takehiko Hoashi) To put it another way, it's a Contra clone, from the weapons pickups to the tank you can drive that's straight out of Contra III, but set in the SD Gundam universe.
Despite the cutesiness of the game, it's still kinda tough, though probably not as tough as a Contra game. The stage design feels a little basic and bare-bones compared to Contra. Nevertheless, it's a very solidly constructed, competently made game and a fun diversion. Just don't expect a subversive take on the genre.