SystemModeler 4.0 does not have complete support for Media and Fluid, that's why those are not included.
However, if you anyway want to get your thermal process simulation package working it may be possible if you instead of including all of Media and Fluid try to identify the components that are used and only add these (probably easiest in a text editor). But, if you need to use the setState_pTX function above it is not sure it will work.
