Ummm no. If you don't spend the whole hour to max it out cause you get bored and do other things and forget about it, then get into battles because you forgot about the EV training, then there's plenty of chances for unwanted EVs to show up.
I know this because I have done this myself.
I mean if you're all about EVs and are super into them, then yeah, you're gonna want to do it all at once. But if you're doing them casually (which Super Training allows you to do) just because you can? Then yeah, it can happen. Easily.