Flux-cheap PD options like PD lasers and LRPD work as you said, being enabled almost always.
But it definitely fails with IPDAI IR pulse:
Spoiler
https://www.youtube.com/watch?v=4HnrJmgE7Ao
Disabled at about 40% flux and let's Sabots through past that point.
More weirdly, Burst PD lasers suffer from same problem:
Spoiler
https://youtu.be/mQfU35ot7u0
They aren't even flux expensive to fire...
As result, PD lasers can't stop Sabots due to range, LRPD due to lack of dps and options that should work mechanically fail due to AI.