Hi Rick,
To answer your questions:
1. Does anyone apply these factors to their every day welding? Absolutely
2. What about adding for root opening? Yes
3. Do you over weld all fillet welds to compensate for all cases? No. Too costly.
4. Do you have the engineer calculate and size welds for all possible joint configurations? Yes
5. Is it acceptable to apply fillets without access holes? I've never heard this question before, but I can tell you that there is absolutely no reason to add extra labor to a project by adding access holes for fillet welds. If you propose all CJP welds, your welding cost will go through the roof. With that in mind, it would probably be less expensive to just add another QC guy to your staff.
I am a Production Manager, and to me, production and quality must really be one in the same. You want to build quality into your products, not inspect it into your products. Back when I first started in the shop, I used to refer to Quality Control as Quantity Control. I have long since realized that it isn't any harder or it doesn't take any longer to do things the way they're supposed to be done. That is, by the code. Our work must meet the minimum applicable code requirements. To me, anything beyond that is overkill, and drives up the cost to produce the job. On the opposite end, anything less than that is automatic poor quality, and is rejected. Our shop guys are trained and educated to the point that they know exactly (for lack of a better phrasing) what they can get away with and what they can't. As someone once said, There's never enough time to do it right, but there's always enough time to do it twice.