When the boolean is resolved and the "create single object" option is enabled, a single object is created from all of the sub-objects and all the material assignments are put onto that simngle object. Now, with the material stacking, we limited the number of materials on one object to 64, because that should be enough for everybody, right? But it turns out that you can get over this limit very easily with boolean objects. In the current release candidate, the limit is raised to 256, but we will remove it altogether soon.