Why does HOMER utilize thermal load instead of energy bill data when calculating optimality?

The idea of HOMER is that you tell it how much electricity and heat you need, and it designs a system to serve those needs at the lowest possible life cycle cost.  It does an hourly simulation of a typical year, and it lets you enter hourly load and resource data if you choose to do so.  Otherwise, it synthesizes a year of hourly data from typical daily load profiles in the the case of electrical and thermal loads, or monthly averages in the case of resource data.

Since you are asking why you can't enter energy bill data, I presume that you have monthly total thermal load data from energy bills.  You can indeed enter that data, but you will have to make an assumption about the daily profile of the thermal load in each month.  Obviously the simplest assumption is that of a flat daily profile.