Luke,
In Simscape, the energy flow rates in and out of a block's ports are calculated based on the principle of conservation of energy. The energy balance equation is expressed as the sum of all the internally stored energy plus the energy that is entering or leaving each port of the block. This includes all forms of energy, such as kinetic, potential, and thermal energy.
The energy flow rates are not limited to a specific equation but depend on the type of physical behavior being modeled. Therefore, energy flow rates may include the work terms from conservation of energy equations which include the pV term or other relevant energy conversion terms.
Regarding the Flow Resistance (TL) block, your observation of a temperature rise across the block is a valid indication that the energy loss from the pressure loss is being conserved via thermal energy. When fluid flow through a restricted orifice, the energy created by the pressure drop is converted to thermal energy due to fluid friction.
Regarding the Pipe (TL) block, the temperature reduction across the block while using a perfect insulator (adiabatic) is not expected, and it's not evident without further details about the model. However, it could be attributed to errors in the initial and boundary conditions or possible assumptions in the modeling process. I recommend checking the model conditions for possible discrepancies or use alternate methods of modeling the same physical phenomenon.
