CDJ75: 1. The PC versions never released in Japan.
2. The PC versions were based on versions that used the english dub, even in Japan. (Integral and Substance.)
SirYodaJedi: According to PCGamingWiki, Substance supposedly does have a Japanese language version on PC.
[url=https://www.pcgamingwiki.com/wiki/Metal_Gear_Solid_2:_Substance#Localizations]https://www.pcgamingwiki.com/wiki/Metal_Gear_Solid_2:_Substance#Localizations[/url]
Was added in a rather recent uncited edit, though, so take it with a grain of salt.
[url=https://www.pcgamingwiki.com/w/index.php?title=Metal_Gear_Solid_2:_Substance&diff=980486&oldid=960818]https://www.pcgamingwiki.com/w/index.php?title=Metal_Gear_Solid_2:_Substance&diff=980486&oldid=960818[/url]
Also, facepalm at their lazyness with lipsync in HD collection.
EDIT - forum software doing strange things with the urls, but you can copy and paste them or look it up manually.
Yeah, I'm gonna cast doubt on the japanese VA. Someone probably included this because the game *has* japanese VA, but the PC version never included it.
Also, just for fun, one specific scene shows the difference off pretty well.
This video is from the japanese PS2 version.
https://youtu.be/-n6rZTK45_8?list=PLaHGcMqqXPv_zKgXJIhkU6rucJrZ-syRW&t=4799 In case the time-code doesn't work, skip to 1:20:00, the close-up of Solidus inside the Harrier's cockpit. Lip sync fits pretty well.
And here's the same scene from the japanese HD collection.
https://youtu.be/5MHLBb6HtRI?t=209 About 3:30 into the video. Game uses the english language lip sync and it doesn't fit.
Strangely enough, I think they did use the japanese version's animations for the codec conversations actually, as the japanese HD collection still has those bits that the US dub is missing. For example, call Otacon from a locker during the tanker episode and they'll talk about how this is exactly like when they first met, just with reversed rolls. Then Snake jokes that at least he didn't piss his pants. In the english dub the conversation just ends with an insulted Otacon, in the japanese version however it ends with Snake bursting out in laughter with a unique laughing animation. And this animation is still in the japanese HD collection.
Can't really find this specific conversation from the japanese version right now, but here, since we're at it, another interesting tidbit. The first game also had different lip sync during codec conversations for both the japanese and english dubs, at times they even used different expressions, for example the colonel might look angry or sad in one version but plain faced in the other version during the same conversation etc.
Anyway, point being, the japanese version has one expression never seen in the western localisation.
First off, spoilers.
https://www.youtube.com/watch?v=l_2_u28r3JY Video is from a patched version of the japanese PS1 version, hence the english subtitles. Anyway, at about 2:30. Angry, screaming Liquid!