I wonder about your wording "by itself".
As far as i know, it is pretty much work of training and concentration to generate a visualization.
But i heard from a beginner in meditation, that he had some vision of the buddha coming nearer and nearer to him until they melt together. This came by itself while sitting in meditation.
He asked my teacher, if he was allowed to meditate like this because as a total beginner he had no initiation. The Geshe said Yes, it is okay.
Maybe it was a memory of his past life practices.
That's very different than what i'm talking about, I was just asking about self-generation as the deity outside of sadhanas, but not in post-meditation.. like instead of of focus on breath etc., you sit for 30 minutes or whatever and do self generation, because i'd seen it mentioned in books like that.
From what i've asked my own teachers, I don't get the impression that it's "not ok" (though I could be wrong, and i'll bet there's different answers), I was just wondering if it's regularly done.