Actually once you orbit around or land on a new celestial body (mun, minmus, ect.) the tourism contracts start requiring orbits and landings on this body too (which I don't think KSTS does yet? But it might be a great future addition!)
However there are multiple kerbin-orbit only missions (space station, satellite, rescue, ect.) where KSTS removes the control risk and player focus investment (remember you still pay the funds and wait the time) of the launch with the exception of these tourism contracts. This just seemed odd to me when I started using KSTS so I thought I'd mention it.
Another issue I noticed alongside the staging is the interaction with other mods that tweak parts. For example the settings for ModularFuelTanks are lost when a craft is deployed using KSTS.