Hi vedor
PixInsight LE does not supports any task for aligment or image integration, but the full standard edition of PixInsight does. It will be avaliable (we hope) at the end of the year, but it will be a comercial version, not freeware as LE is (and will be).
With PixInsight STD you can perform the hole process. Right now it includes a Dynamic Aligment Tool, that registers two images using sample points (stars) that the user must specify. We are looking for automatizating that process. Anyway, the results using this tool are very good, with subpixel accuracy, and can handle distorsions very aggresive. Of course that it works with images of different sizes/resolution.
Then, we have another tool named Image Integration, that performs the median or average of multiple images (any number you want), using some rejection techniques like the well known sigma clipping, MIN/MAX, etc.