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It's a joke.
And please don't fucking bunch Japan with Sex just because "HENTAI OMG SO PERVERTED"
If he were to put them in because of the latter, it's a cultural thing. (^Watch video above^). Japan is just much more tolerant of sexuality in games than the west is, so putting in a little easter egg like this is essentially a harmless joke, even for gamers of the youngest demographic in Japan, but in the west I guess it's just suddenly perceived as "Pixel must be perverted because he's Japanese".
Bringing it up at all makes you look like a moron, and this is regardless of knowledge on or about the reason behind it in the first place. It just makes everyone look bad.
Way, way back in the day, Japan didn't really have undergarments outside of royalty, or at the very least nothing sexually specific. Then came America. America dropped an A-bomb, and Japan sort of developed some kind of weird Stockholms syndrome / fanboyism for America and its developments.
Panties, for whatever oddball reason, were actually a very expensive import from America to Japan, as a new garment specifically for women. As a combined result of American fanboyism through the culture, and the high tangible value / low number of these garments in circulation, ownership of them became equivalent to being the cool girl at school. This was then amplified by Japan's cultural belief that all objects are themself living things, and therefore the rare and expensive object must have the soul of royalty in itself.
So in effect, consider panties in Japanese culture to have started out similar to finding a silhouette of Jesus on a piece of toast. People will flock to, and worship it, like their lives depend on it.
As for portrayal in present media... I don't fucking know, and I don't want to know.