Tom: I've never dealt with a Self Directed IRA directly. However several clients have come to me with schemes to use one for a rental property, or even to invest in a franchise business. It seemed really popular among some franchising companies a decade or so ago - the franchising company would ally with a S/D IRA administrator to promote this as a way to buy into the franchise. (Maybe they still do).
After reading a little about the rules, and studying a few stories about how these schemes failed, primarily over "prohibited transactions" as you mentioned, I decided to never touch one. I learned just enough about them to avoid them like the plague. I'd just tell the client that if they moved ahead with the plan they would need to find another accountant. Furthermore, I knew someone who was scammed by a financial advisor who set up a promissory note in a S/D IRA that even their family didn't know anything about until it blew up in their face.
So I have a strong bias against these contrivances. Not saying they never work or there isn't a place for them, but there's too much room to get tripped up by seemingly minor mistakes as well as lots of room for outright abuse.