Skilled players don't need the extra information from the upgraded Tracking Station, and they probably don't need SAS, although I've found SAS to be a big help in stabilizing the craft. Alas, I'm no skilled pilot, and with version 0.90 those unmanned command modules suddenly become very attractive for launches without a Kerbal pilot. In my current game I wanted a Kerbal scientist in orbit, so there was no room for a proper pilot. Self-imposed challenges and restrictions are a lot of fun.
Indeed they are!
I took on a challenge in my latest hard carer, to never take a random contract before the scripted ones are all complete. Getting the Minmus intercept with my probe was a bit hairy, but it actually got quite easy for a long while after due to access to nodes. So I made the restrictions steeper, I now can't upgrade any buildings apart form the ones needed for manoeuvre nodes and if possible I want to put Stayputnik's on every body in the solar system.
Which leaves me with relatively early tech, sub 18 ton, 30 part rockets and no SAS with which to land on every planet (bar Jool) and moon in the solar system!
The Stayputnik drones have gone to many places so far,
The Mun, Minmus, Duna, Ike, Gilly, Jool, Bop and Pol, With more heading to Dres, Vall, Laythe and Tylo currently. I've had a few mishaps, like running out of fuel at Ike, Gilly and Tylo, and a 7km/s flyby past Moho

...
Unfortunately, effective piloting of the thing I came up with for future missions to Tylo and Moho is, well, pretty much impossible. I can reliably get it to orbit, but the dV left when in orbit ranges from 5800 to 7200

I'll have to see if wings or something can help stability as it tends to spin and wander. A lot.
I indeed used the atmospheric ISP in the calculations. Your "9 FL-T200" craft has 4190 delta-V (atmospheric) and 4845 delta-V (vacuum). I mostly use the calculations to check if the craft design makes sense and if redesigns make any drastic changes. The way I understand it is that the delta-V changes when fuel is burned, so calculations are approximations at best.
Actually when in a stable orbit dV is pretty damn accurate, as the equation takes into account the mass changes that happen during a burn. Getting out of the atmosphere however, does require a somewhat unpredictable amount. Mostly depending on your throttle control and flight path due to atmospheric and gravity drag.
I personally like the standardised conversion of 4550 vacuum dV to orbit, which takes into account a lot of the losses expected when flying well, as it gives me some feedback on how well I did actually fly.
Yeah, that's not quite the reusable SSTO I had in mind.

I don't think you can expect a fully re-useable SSTO which can achieve anything beyond that goal up until jet engines and 48-7s, at that point, rescue and light satellite launching SSTO's will both probably be achievable. You can go the the Mun and come back with fewer than 30 parts and while under 18 tons afterall!