Self-intersection issue when converting polygons to boxes

I have been using this tool to annotate images.
Unfortunately the web-based tool differs significantly from the Matlab code in terms of how it converts polygons to pixel maps. The LMobjectmask function makes use of Matlab's poly2mask. This function does not allow self-intersection of objects and removes pixels that are covered twice by the same object. This is not the case for the web tool.

It would be very helpful if you could provide Matlab code that matches what the annotators see in the web tool.