You will find that pyrocat negatives do look slightly thinner, but it's misleading due to the staining of the developer. Use your densitometer to get in the ballpark (which it appears you've already done), but let the print tell you if you're on the right track. How are the highlights? Too white, too gray? Adjust development accordingly.
Please don't get fixated on the 0.1 over fb+f standard - I used to do this, and more often than not my shadows were quite weak. I would suggest placing the shadows on a higher zone to get them well off the toe of the film - you'll get better separation in the shadows, and you won't block up the highlights since todays films have such a long straight line section. For standard emulsions (such as Tri-X and HP5+) you probably won't start hitting the shoulder until zone XV. Yes, you're printing times will be longer, but so what?
When you meter the shadows, you're reading an area, and sure enough some of the shadow areas will fall on zone II,even though you meter it as zone III, assuming of course that the shadow area isn't one single tonality, very evenly lit - by moving the shadow exposure up the curve, you'll get the darkest shadows on III, giving you more separation, and therefore richer detail in the shadows.
Good luck! Pyrocat is a great developer - I've used it in the past, and I'll use it in the future.