This is relatively standard financial shell games, actually.
The same offers are often available when refinancing a house, but it just gets called "closing costs" or "document fees" so it feels a little bit different... also partly because the numbers FEEL bigger for a house and so ppl just sign on the line.
What's going on is that the lender has done its calculations and decided once upon a time that it would charge $299 to cover costs with loan refinances... No big deal. I trust that you're comfortable enough with reimbursing them for that.
As far as adding $1000 cash now!... and having you pay that back as the loan, they're doing some fancy financial calculations. If you want to see what that would basically cost to compare with an immediate $299 payment, you need to do some moderately complex financial calculations.
Here's a ballpark, but I'm making some assumptions that could get closer if you gave the new interest rate and the loan terms. Assuming you got a new loan for 13,000 at 3.5% for 5 years (60 months), your new payment would be about $236 per month. Check out bankrate.com's car payment calculator if you want to follow along.
That means that with your new loan you'd pay (60 * $236) + $299 = $14,459, if you went with the up front fee.
You'll pay back in principal 14,000 for the loan if you take the cash up front, which is $255/month or about $15,300. The obvious difference between the two is 15,300 - 14,460==840.
Now, how you evaluate it from here is up for debate and PhD thesis papers, but here's my two cents. You'll have to pay 299 either way to refinance your loan. So you're only really paying $540 extra to do the cash up front. Do you have the 299? It would save you money. Could you use the extra cash now? (And carry the higher payments?) Maybe the deal makes sense.
Its up to you. But I would be careful with respect to refinancing frequently, especially if you're at the first year(s) of the loan. The way that loan repayments work, you end up paying mostly interest up front and then start repaying your principal more and more towards the end. So you may feel like you're saving, due to the lower rates, when you're actually paying mostly interest perpetually without making a big dent in your loan balance.