No, polyurethanes, silicone ect wont hurt epdm. Any type of roof cement or oil based product would though. The caulk is used after the adhesive for a temporary seal until the glue cures and for T bar, Boot tops ect. Regular (cured) epdm will not form through angle changes or around pipes and such things. Thats what the uncured form flashing is for. Its also used for T joints, vertical patches, curb corners ect. The material on the stack and gas line in the pics is form flashing as is the strip in on the boot. They used to use neoprene but it ages and splits.