No one here has actually dealth with MS to know what happens, eh?
#1. You don't send your HDD, just the 'box. The HDD stays with you, and has every bit of information on the HDD, so getting the refurb does nothing, you keep everything. The only thing that needs re-done is re-syncing the controllers to the HDD.
#2. There is no 90 day warranty on the X360, it's 1 year. I do believe the refurbs are 90 days, but I am unsure. You can always pay like $25 and get an extra year from MS.
#3. If something like that fails, do you really expect them to ship you a new $400 system? If so, it'd be easy to force a failure on a 360 and make 'em give you a new one if you didn't like your old one. I have a refurb, and it plays better than the new one I owned.
#4. The reason MS does refurbs rather than send your own unit back is 2 fold. 1. They will actually send it back to you (your unit) if it's quickly fixable. I assume if the RROD is because of the sauder issue, then they send a refurb and fix it in-house to cut return time. In my case, I got a refurb shipped to me in 1 day of my 360 arriving at MS's repair center (I got my 360 back before Alarcist's wii, but my died later, and I took longer to send mine in)