I would have asked politely. And yes, it would have been preferable to use the store toilet. However, if the clerk said no, I wouldn't interpret it as 'flak.' My choice would not have been to use additional minutes to harass and threaten the clerk who was just trying to follow the store rules. I would and have swooped up my child and hurried to my car where the accident would happen on my property or on me while I carried them, where it was on me to clean up. And if I had "bawooosh" on me, then my shopping would be finished and we would go home. (I always had a change of clothes for the kids in the car in case of accidents when they were young.)
But then, raising 3 kids, I never had an accident so bad that it would be all over the floor. I have had blowouts that were all over the underwear, surrounding clothes, and down the leg. I have held my child where urine or diarrhea got soaked into my clothes and into my arm that was holding them under the butt. But I don't see any reason to threaten anybody that your child is just going to stand there and go ahead and "bawooosh" all over the floor.