I note that the Hydro Inputs window has the option to “Simulate systems both with and without the hydro turbine”. Why is this option necessary? Won’t HOMER by default rank the systems according to cost so that it will be seen whether or not the hydro system is cost-effective? This is what obtains in the case of the PV and wind turbine systems i.e. there is no option to “Simulate systems both with and without the PV system (or wind turbine)” yet HOMER generates solutions with the PV system (or wind turbine) and solutions without the PV system (or wind turbine).
 
I also note that there is the option to “Include the hydro turbine in all simulated systems” which seems to suggest that none of HOMER’s optimization solutions may contain the hydro turbine however, it may be compulsory for the hydro turbine to be included in the system’s design and this option will therefore ensures that it is. Again, this option is not given in the case of the PV system or the wind turbine, yet it may be compulsory for these systems to be included in the system’s design.   

I perhaps am misinterpreting the meaning of these options.

The format for the inputs of a the Hydro turbine are indeed different from that of other generators in HOMER. 

Selecting the radio button labeled "Simulate systems both with and without the hydro turbine" is equivalent to adding a "0" in the sizes to consider for PV, Wind turbines or other technologies.  HOMER will rank all of these systems according to their NPV as usual.  Selecting the button "Include the hydro turbine in all simulated systems" is the same as entering only non-zero values in the Sizes to consider table.

You can ensure that HOMER includes, for example, 50kWp of PV in all systems if you enter only the value 50 in the Sizes to consider table on the PV Inputs window.  If you also enter a "0" then all systems will have either 0 or 50 kWp.

With the Hydro turbine, rather than entering various values in a Sizes to consider table, you can compare different turbine design sizes through the various sensitivities (design flow rate, available head, efficiency, etc.) on the Hydro Inputs window.