Umm, I saved 59/60 on Wakazashi 6 - Paradeath. However, the second set of fire traps don't affect your lemmings, so that is probably why that was possible. (Ahribar, it is very dubious to assume that the maximum possible has been reached simply because every skill has been used, but in this case it is likely just a case of a defective trap.)
Also, I'm not sure if this has been pointed out, but Kozuka 15 - Falling Out is bugged in that all of the exits are functional (I think this is a Cheapo limitation). To work around it, you'd need to update the style to have a decoration object that looks like an exit.
Hm. Do you know any surefire way to trigger that builder replay glitch? If so, our 100% solution is found.
Generally, a solution that requires a Cheapo replay glitch (builder, window order, or otherwise) is not considered legitimate.
Oh, and the surefire way to trigger it is to do some pixel-precise moves correctly, then make a small goof at the end of the level. Then, you'll find out in the replay that the builder timing glitches and you have to start all over!
More seriously, it tends to glitch when you pause a lot and/or assign skills during pause. I have no solid evidence for this, but just my experience.