I've now that I've been using the 40-100 flats, that Dunlop sent me, for about a week. One set on my JB and the other on my new '58 type PB that I just finished building.
To answer your question, these string set did intonate, yes.
A few other observations:
The pop-creak issue:
I've figured out that pops or creaks originate around the ball ends of the strings, not surprisingly, and there is an issue involving friction but it's at the bridge, not the nut or nut slots. I believe the cause of the unfortunate amount of friction is probably unusually long silk ends that extend out at least 1" from the ball ends. That's compared to roughly 5/8" on Fender 9050L flats. Because the silk ends on the Dunlop flats are so long they ride over the top of the bridge saddles and beyond the witness points. There's no such issues with the one set of Fender 9050 flats I'm using on my other P bass (Nash PB).
I don't know why Dunlop makes these strings with such long silk ends but I think it's problematic.
Ease of setup and use: Based on my experience Dunlop stainless flats are on difficult end of the spectrum getting them set up; intonation and settled in to hold stable tuning. By comparison setting up new Fender 9050 flats seemed routine in this regard. There were no surprises; easy.
String flexibility: I think the Dunlop 40-100 flats feel a bit more flexible than Fender's 9050 40-100 flats. I prefer the amount of stiffness in the 9050 flats. I think the general stiffness of Dunlop stainless flats in 45-105, rather than 40-100, is more to my preference.
String finish: The outer winding on Dunlop stainless flats is tight and polished smooth. The outer windings on 9059 flats aren't as tight and the finish isn't polished. Fender flats are dark grey in color with a flat sheen and a bit of texture that I actually like, probably because I've used rounds for so long.
Tone: The Dunlop and Fender flats don't sound drastically different to me, for what it's worth, but there are subtle differences. It's hard to judge because I'm using a set of each on two different P basses, Dunlops on one and Fender on the other. The differences between the two P basses I have are substantial enough to cloud the matter of comparing how the strings sound. I also need more much time using both string sets to see how they mature or change over time; months, not days or weeks.
Overall: I think the Fender 9050 flats are a better sorted out product than Dunlop's stain flats. I think Dunlop has room to make improvements, including eliminating whatever what could be the cause of intonation problems (they've evidently had similar problems with other strings line they make) and by making the silks at the ball ends shorter so they stay clear of bridge saddles and witness points.