Number 1: Yes your rooster will breed with all of them
Number 2: Spots in eggs are usually because you have a rooster in with your hens...and no they are not bad for you,
but most folks react the same way you did, and have reservations about eating a fertilized egg.
Number 3: Whenever you have a situation where you introduce medication to livestock...there might be a period of
time that you shouldn't use any of their products. The package should give you the proper period that the
eggs can't be used....or I would suggest Googling the product, and getting a more complete label.