PDI is just part of the dealer's overhead. They may have accounting reasons to make it a separately listed item, or it may be a way of adding additional dealer profit. Probably both. Research what is a fair price and make your offer the full price, plus tax & title, nothing else.
Car dealers used to try to shift some of their overhead to buyers, adding an "advertising charge" to the invoice, or on really popular models even adding "additional dealer profit". No need for buyers to make that part of their offer. As always, if a dealer can sell a unit for more, he/she will do so, but buyers can set their own limits, too.