Hi JJ, if you think back to when you've purchased a car from a dealer, new or old, the final number is always a LOT more than the advertised price. Buying the Elio will be no different.
I've read a delivery fee of around $750. I calculated costs of me renting an economy car, driving to Shreveport, staying probably 2 nights in hotel, food, gas, and then driving the Elio back... from where I am, it'll be less expensive to get the car delivered.
For the base price (what we've called in other threads on the forum, the Paul Elio Price, or PEP) of $6800, EM has been forthcoming and said that they are at $7100 now, doing their best to whittle away and get the price down $300 more.
To answer your final question, I agree with Craig: I don't have any concerns about surprise charges. Options you get on your Elio will drive up the price, there is title, license, tax, etc. We do have lots of time, so you can gather the tax rate, the title fee, the registration costs, and get your own estimate to satisfy your curiosity.
But no I don't anticipate $299 to paint on a pin stripe, extra strange fees just to drive up the price. etc. EM has said that the buying experience should be direct and brief by today's standards. "You want a blue manual transmission, with cruise control and leather seats. Great. We're done!"