It is specific to some degree, if your seller is a developer he may be more inclined to give you more of a concession on costs than price for the reason stated.
Beyond that, it usually comes down to how an issue of how much cash the the buyer can come up with at closing. When the seller agrees to pay 3K additional in closing costs and you agree to pay 3K more you are really rolling those costs into your loan. I know that is not really your situation, but that is how the issue comes up the most. (Edit: maybe it is).
As for your real question regarding loan to value -- I may have picked a bad example to work with:
House -- 100k Money you have 13 K
He agrees to lower to 97k
You put 10k in the house and 3k toward costs
LTV = 89.7%
_____
House stays at 100k, but he pays closing of 3k:
You put 13K in house
LTV 87%
Am I missing something??