...the "villain" in question is more of a misunderstood anti-hero, with a soft spot for our hero, and an actual heart of gold buried in there somewhere.

Oh, yeah, now that is an interesting dynamic! (Though only provided said hidden heart of gold has strong canon evidence and isn't just pure fanon ^^) A canonical anti-hero x anti-villain scenario is one of those rare dynamics that can turn out fabulously, in the hands of a good writer.