According to the manual, weights are calculated based on the inverse of the scale factor - i.e. it takes into account both the sub duration and sky transparency but not other sources of noise:
Quote:
Weights
Weights are calculated from normalization as the inverse of the scalar factor. The combine procedures use these weights to optimize the resulting S/N.
Changes in gain (due to different cameras in the same stack or variable gain due to binning) are factored into the weights so that all of the images are normalized on the electron level. The gain of the reference image (top image) is used to normalize the other gains (if different) and this affects the weights.
For example, after normalization the average ADU of a 5-minute exposure will approximate the average ADU of a 10-minute exposure (that’s what normalization does). If these images are summed without weights then the 10-minute exposure will contribute the same S/N as the 5-minute exposure, thus resulting in sub-optimal S/N. But a weighted sum preserves this difference to produce optimal S/N.

The weights are shown in image manager. It is possible to override a weight by entering a new weight in the image manager form. One possible reason to modify a weight might be to decrease the impact of images with poorer resolution.
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http://www.ccdware.com/Files/ccdstack132.pdf