All that can be adjusted in a typical tire shop as far as alignment is concerned on your ITR, is the toe. Hondas have no camber adjustment available except if you install camber kits.

As far as the extra charge, most alignment shops have a set time for doing an alignment and if your car is lowered and they need to use wood blocks to raise it, this requires more time thus more $$$.
An ITR with sport springs is standard height and should be aligned with no difficulty.
If you were to compare the job vs. a Passat 2000, where there are 4 upper ball joints and lotsa of alignment adjustment, the price would be almost 20$ more.