why does it seem like the RRS holds it's value more?

Land Rover made a lot of improvements to the 2007 HSE so if you compare prices of the HSE and the Sport for 2007, you will see the price is more for the full size. In my area, the full size 2007 HSE goes for more than the 2007 Sport Supercharged.

I noticed that also, and I think one of the reasons is because the RRS has only been out since 06, so the design is a little bit fresher and has more street cred than the RR, which has been out since 03. There are a lot of tired looking Mark IIIs on the road already, which diminishes the perceived value of the model. But like you, I agree that the full size is the superior vehicle. It has that tall aristocratic "to the manor born" demeanor and far plusher interior appointments, although most of the people I know prefer the more aggressive styling of the Sport.

Watch what happens to the value of the pre 2010 RRS now that they have fixed the cheap looking interior. 2007 HSE RRs on will have higher values than the RRS IMO.

That's generally the case with all brands. The top of the line models tend to have the lowest residuals. I think part of it is that you have a lot of other options (new and old cars) at the $45-60k price range which is what a new $100k car will be worth in three years.

Absolutely true. The RR is 2002 or 3 of origin, and the RRS is much fresher car.

A normal median would work here.
MRSP RR / All quantity of 2002 or 3 (I am not sure) - 2009 comparing to MRSP RRS / 2005 or 6 - 2009 is really different.

Do new buyers of RR really feel the difference between 2003 or 2007?

No. I don't think so.