So how does NTSC-Japan's IRE 0-100 (0-235) fit into this laserdisc capture for NTSC-US IRE 7.5-100 (16-235)? In the capture or post-processing?

That's a good question. The capture levels I used were set using the color bars and ramp from the Video Essentials LD. I think AfterEffects converted the image to RGB using 16 as the black level, and it looked fine. Actually I lowered the shadow blacks a bit because blacks were almost always above 0%.

One possible explanation might be that the transfer was made in the US and they reused it in Japan without conforming it to IRE 0 black.