It has been discussed at length on here, and there are several points of view.
I think you would be sensible to use the suggested screws, for maximum joint strength and much less risk of joint damage. There are others on here who even swear by ornery countersunk jobbies.
It's almost a
[shsssh!]sharpening[/] debate.
If I dare sum up:
- The joint is pulled together almost, but not quite, at the correct angle by the screw(s). Even in a correctly-made PHJ there are forces trying to move the joint out of alignment when the piece is finished. almost, but not quite means that there are, admittedly small, forces at right angles to the "hold it tight" one. If not well controlled these can cause misalignment, gapping, or even joint failure. This is why you should clamp the joint tight before driving the screws. Aside: I have tried not doing this when in a rush to make something that doesn't matter (e.g. a clamping frame): it didn't end well.
- Glue may be used, but at the end of the day, it's an end-grain-to-face-grain joint with very little glue area. It is a fundamentally weak joint, relying on the material strength much more than most other jointing systems.
- The head of the screw is basically going through end grain and pulls on it along its shearing/splitting axis, to hold the joint together. The thread end of the screw might be better, as it's into face grain, but that depends on the thickness of that component. The thickness limits the screw depth*.
- Any countersunk screw head in this context acts as a wedge, trying to split the thin and weak end grain between the pocket hole itself and the mating part of the joint.
If you are not stressing the joint, for example just using PHJ to hold a face frame together or onto a strong carcase, the above probably doesn't matter. On the other hand, if you are using pocket hole joinery close to its realistic maximums for joint strength, and/or there are reasons why the joint might be stressed in use (note that PHJ often uses no glue at all, relying on the screws alone), I'd say using the right screws can be critical.
As I said in an earlier post, the reason for the flange is to get as big a bearing area onto the end grain as possible, and to not cause a wedge with the associated splitting forces.
OK, tin hat on head, heading for the bunker now... (hammer)
E. (who likes pocket hole joinery and uses it, despite its limitations)
*Kreg chose screws with an axial cut down the point, so they can get closer to the visible surface of the face-grain material without blowing out the other side -- useful when using the system in chipboard, etc. It's another good reason for using their screws - you can get the maximum screw depth possible when doing carcases.