Your post provides some valuable insight into some of the downsides of a HUD loan. You are correct in that on a purchase, the fees associated with the loan are "tacked' onto the rate so you will end up with a rate higher than what you are quoted. The HUD analysis that is provided prior to engaging the lender ought to cover that point, but there can be some sticker shock when you think you're getting X, but in reality, it is X + Y, and Y can be as much as an extra 1.75% to the initial rate.
However, that is not an an issue on a refinance as almost all of the costs associated with a HUD loan are mortgageable. That means the rate that is quoted is the rate you'll get, and last time I checked, that rate is in the 4s.
The upside to a HUD loan is a having a long term loan (up to 35 years) with a high LTV (up to 85%), and on a non-recourse loan. Not to mention, HUD is one of the only places you can go if you need to do a cash-out refinance (up to 80%), rehab, and construction. If you are in need of any of those, HUD is often your only choice.
In my experience, HUD is best suited for large properties in the 5M and up category. When you get into properties that are in the 2-5M range, I think there are other financing options that are better suited for those properties.
Is HUD perfect? Not by a long shot. Like most things in real estate, you have to weigh the pros versus the cons and measure that against what you feel is important to you as a borrower.