There are many elements to your question.
In terms of comparing bids, typically a government would decide in advance whether it wants to have an asset tolled, for example, or to have some sort of levy that would be raised against its expenditures. Different bidders would propose a user fee or not, depending on their bid. Basically this is a government decision. The procuring jurisdiction would have to decide whether they want to have a certain asset being tolled or not.
In terms of whether a user fee is assessed as a cost to the project, it's more of a revenue source than a cost, so I'm not quite sure I understand your question.