I came here to say the exact same things. Two issues, with easy fixes:
(1) Any other game I would expect her "perfect" hitbox to be forward of where it is and the actual perfect line to be taking damage because I'm overlapping an enemy. As a concrete example of the result, my gameplay gets worse when I'm looking past the middle of the screen on one-sided attack sections. This is after tuning multiple times using the delay tester with my eyes closed. Moving her back from the line or moving the line away from her (to gain appropriate separation between her and the "perfect" hitbox) would fix it.
(2) Also, yeah, all of the multi-hit enemies are lacking in sufficient cues. The fact that they're already at the line makes it seem like you should insta-attack them because they're already at the "perfect" distance; this could be solved by having them knocked back to the distance of the next beat you're expected to attack them on.