Hi Miia,
First, congrats on doing research and finding blogs that provide helpful information! I'm curious as to the editor who told you to never submit a paginated manuscript? Is it a freelance editor or an editor at a publishing house?
I write picture books. I've submitted many of them. As a rule of thumb, as Carol Hinz said, most authors don't submit paginated manuscripts. However, as she note, she likes to see them that way, as I do know other editors and agents don't seem to mind. But I think the general advice is to NOT paginate them as it might appear you're trying to do the editor or the illustrator's job.
BUT, I think it is very wise for you to WRITE your story that way. You want to be sure you can envision illustrations on each page spread. It's a great way to build in great page turns. (I often indicate page turns with an . . . then a new paragraph.) But most of the time I remove the page numbers before I submit. Occasionally I'll have a story where my agent asks to see the pagination so she could see my vision for the story if she wasn't quite "getting it."
So don't panic. It was just one editor's opinion. Most agents and editors just want an easy to read manuscript and if you submitted it that way, I can't imagine that most care that much. Just be sure that you're willing to be flexible if the book gets acquired - the editor and art director may change things up. They are the experts.
I hope this helps!