I was going to take a shot at this question, but I don't have a current copy of D1.6 and fear the paragraphs could have been revised in later editions. Basically to be brief, for the PJP joints you would subtract an 1/8" from your depth of bevel to figure your weld size. Having said that, you still need to mock up the joint and weld it, then cut and etch to make sure that you are indeed getting what you called out for in regards to your weld size(IOW, verify the depth of penetration).
If you are using a prequalified joint detail like the B-P1a and you follow the tolerances, you will most likely get an acceptable weld due to using the time tested and proven prequalified joint details. Enough of these joints have been welded and tested over the years that AWS feels confident enough to publish the prequalifieds for you to use without asking you to perform all of the qualification testing yourself.