Joel, A few things to back up some of what the guys have said. Also, I think your questions will be answered in our PIP-1 'Stack' tutorials you just ordered.
BPP is very good, and 'calls out' to the other independent modules to do its work. While it is powerful, one limitation is that you can only use one master bias or dark, so if you have varied exposure times or temperatures, you'll have to choose only one.
Additionally, it allows for only one pixel rejection algorithm for light frames. So if you have say 9 subs each for color channels, but 20 for luminance, you would again have to choose one algorithm, to the detriment of either L or RGB. These are the reasons why integrating with ImgIn may be better. Also, though BPP offers the same control as ImgIn with regard to Sigma rejection sliders, it can't use a premium, user-selected reference image as can ImgIn.
BPP calls out to Star Alignment and ImgCal so for those functions, the results may be equal to what you can accomplish with them independently. So, while you may be well pleased with the BPP produced masters, many of us use BPP to generate the calibrated, cosmetically corrected, and registered subs, then integrate with ImgIn.
As to your question on CosmeticCorrection- this is very different than calibration. After light frames have been bias corrected, and/or dark subtracted, and flat divided (or not!), CosCor takes care of nonlinear issues such as hot pixels, and also user-defined column defects. Take the time to create a template for each camera. Post calibration, the artifacts mentioned are 'filled in' with the average values of the surrounding pixels. Whether called out by BPP, or run separately after ImgCal, watch CosCor make residual artifacts disappear!
Using darks or not is your call. It has been demonstrated that using darks with some of the low-noise sensors (Sony Exview/Super HAD) can indeed be more trouble than they are worth. If using flats however, you'll need to take at least a master bias.
Nothing wrong with using pre-made masters when using BPP, whether generated by BPP or independent modules.
Lastly, as you 'd see in Jordi's PowerPoint, or our tutorials, noise quotes can be read by the Process Console or the Noise Evaluation or other Scripts.