I suggest you to go to the PixInsight forum to express your wishes (1) and (2). For (1), I think the current BPP covers DSLR very well and nothing has been compromised. On the other hand, I do agree with you on (2). I once told them to allow flats to have a different set of bias. This can be used as bias, if flats are taken with different ISO, or flat dark, as in your case. My request was discussed in the forum, but never implemented. If more people go there and make a similar request, they will consider it more seriously.
For your original question, I think one key is in the "Image Integration" tab in the ImageIntegration function. Many of the options there are not in the BPP integration. For example, if your images are taken under varying sky brightness or varying transparency, ImageIntegration can match their brightness/contrast first before integration. This is essential for drizzle integration. Also, ImageIntegration can measure the noise property of each image and weight the images differently according to the noise. This can lead to optimized S/N in the stacked image when the images are taken under very different conditions. For example, if we track an object from zenith to 30-deg elevation, we would want to weight the images taken near zenith more, as there the sky is darker and more transparent and seeing is better etc. Also, if we have two sets of images, one taken in a dark place, the other taken in light polluted area, ImageIntegration should be able to automatically down-weight those taken under light pollution and give an optimized stack.
In the principle level, what ImageIntegration does is more correct and optimized. In practice, I haven't verified that the end result is better than the simple integration in BPP. However, a couple of years ago here on this forum, someone demonstrated that PI's ImageIntegration gives much better results than that from DSS, when images were taken under different conditions. I think the same will apply to PI ImageIntegration vs integration in BPP.
I think if your images come from a short imaging session (an hour or two) when the condition is very stable, the BPP stacking should be sufficient. Otherwise it should be better to go to ImageIntegration and let it handle the images taken under variable conditions.