In the Isothermal Liquid domain, the density of the fluid is a function of the pressure. See this documentation page: https://www.mathworks.com/help/simscape/ref/isothermalliquidpropertiesil.html. So as the pressure changes, the density also changes, and to conserve the mass flowrate, the volumetric flowrate will change a little bit.
This conservation of mass flowrate vs volumetric flowrate is indeed the major differences between the principles for the isothermal liquid domain vs the hydraulic domain. You can read more about it here: https://www.mathworks.com/help/simscape/upgrading-hydraulic-models-to-use-isothermal-liquid-blocks.html. Conservation of mass is more physically correct, (hopefully that's obvious).
At the outlet of the pump, the pressure is the highest, and so is the density, so the volumetric flow rate will be slight lower than after the pipe, where the pressure and the density dropped a little. I would say what you observed in the change of volumetric flowrate is reasonable and physically more correct than it not changing at all.
A few other comments on the model:
1) the PS-Simulink converter allows you to specify a unit. You can type any unit or combine units together, as long as it makes sense. This way you won't need the gain block to correct the unit.
2) that pressure sensor doesn't look right. Across variable sensors (pressure, voltage, velocity, temperature ...) measures the difference between the A-B ports. So you connect them across two points to measure the pressure difference. If you want the absolute pressure, you need to connect B to an absolute reference block (there is one in Elements in each domain). The newest version of Simscape allows you to skip this reference connection and specify absolute measurement in the sensor itself.
3) I guess the purpose of using the Hydraulic-Isothermal connection is to use the liquid properties from the hydraulic liquid block? If the isothermal liquid fluids property block doesn't contain the liquid you want to use, you can query the property from the hydraulic liquid library using the "sh_stockfluidproperties" command. See more details here: https://www.mathworks.com/help/hydro/ref/hydraulicfluid.html. You can then put the viscosity, density, modulus numbers into the isothermal liquid property block to get the same physical properties.
Hope this helps.
