Thank you, @imagejan!
And thanks for your comments/suggestions. Helps to look at it with fresh point of view!
1a) The calculated area is indeed the thresholded area, after dilation/erosion. I will add more detailed description. Plus if the thresholded spot is larger than specified particle size, there is local maximum inside it and “Include larger particles” is off, it calculates the area in the squared rectangle (i know, it is not very straightforward, but it helps to locate spots that are very close to each other).
1b) Integrated intensity is measured in the following way. First, average intensity over perimeter of bounding rectangle is calculated, it is background intensity, I_{bg}. Then I calculate sum of intensities of all N pixels inside the rectangle S_{in}. To get the final value, IntgInt=S_{in}  I_{bg}*N. So from each pixel intensity I subtract average background value. This method is similar to the one described in this paper. I will add more detailed description of it.

Yes, development of true 3D is possible, the only problem is that I don’t have a dataset to play with. If you have one, send it to me.

Number 1, it is just the distance between centroids and the threshold (max distance between colocalized spots) is user provided parameter of plugin (see this dialog, below). I will try to adjust the description to explain it more clearly.
Yes, I should devote some time and switch to Maven (now I use Ant builder), thanks for the kick!