First, I would reassure you, as did one of the other responses, that counting will not impact is perception like/dislike of math. In the mind of the child, one is about time and the other is altogether different.
Second, I would actually suggest reversing your counting. I know it seems like a simple difference and in the end - even to a child it isn't a big difference, but 3,2,1, does actually work better in my experience (preschool teacher and mother of my own).
Third, I would also suggest that perhaps it isn't a problem of your child not understanding that you "mean business" but perhaps he is hearing "no" too much.
Please don't get me wrong - kids need to be told no, AND yours needs to stay out of the toilet, but one of the problems parents run into is when we say no too much it loses its meaning. Think about it, when you hear a word too much, it stops meaning very much. What curse word do you hear most often? Does it sound as jarring to you as a curse word you rarely hear? I say "come on" to Alice all the time and it does absolutely nothing to speed her along, but if I say, "we've got to go quickly" she totally kicks it into gear (I need to be in less of a hurry with her is what it really comes down to for me). With things like playing in the toilet, your child might just be bored and need some redirection (offer up something more satisfying to you that will be fun to him to replace the toilet), whereas with running into the street you need an immediate response if you say "no" or "stop".
You might like my article, "the magic of toddler water play" if he likes splashing in the toilet, you might get a few "replacement" ideas with which to entice your little gentleman. pinchxeverything.blogspot.com
Good Luck.