I have a sneaking suspicion that stuff wasn't done by Japanese people. I think the more awkward stuff like the JP SCV4 box art was, however. Wasn't the Mega Man 1 U.S. box art done by Americans? I remember hearing that on a documentary, but I could be wrong.
Other than the ambigious anime designs like Sonic and Mario, japanese boxarts are actually a recent trend that occured in the late 90s. Before that, videogame companies would use american artist to grab the attention of the gamers. This was before anime was mainstream, so having anime characters on artboxes back then wouldn't attract people to the title.
Konami is one of the few companies that had good US boxart. I don't think any of their us designed boxart were bad. Even their Goemon turned out cool. Capcom, unforuntately didn't
They mostly used US art back in the 90s. Even their post Megaman 3 covers were done by americans. They just alter bits of megaman's face to make it more western.
However, not every artboxes back then were good. A lot of the US boxes were terrible since the virtually all characters were drawn in a realistic adult style. I think a lot of people complained, which promopted the companies to use the japanese covers.