what you will find isn't a variance in invoice price itself, it's a variance in how different places and dealerships and people define invoice....
invoice is invoice.
however, dealership a may give you an "invoice" price which is less holdback, while dealership b gives you the true invoice price. or maybe dealership c includes destination fees as a part of invoice while dealership d doesn't. and so on and so forth.
as far as manuals costing less, i think for a long time a manual was viewed as a way to save gas and as a way to get a car that you may not be able to afford if it cost you another $1,000. the fuel ecomony differences are negligible now days, depending on driver, so that no longer plays into the equation. but i still do know people who have bought manuals because they didn't want to pay extra for an automatic.
by the time you reach acura levels, the manual drivers aren't seeking out the $$$ savings. the manual drivers are typically enthusiasts in the higher priced cars. i'm guessing that car manufacturers know that and feel they can easily get away with the same price on the at's and mt's. they don't need the "cheaper" selling point any more.