In my view security deposit is your money. Landlord has no right to any part of it unless landlord complies with CC 1950.5.
I don't think cashing that check for partial payment waives your right to challenge the statement of accounts even if it the letter says payment in full.
Please consult your attorney on this issue to better determine your rights.
It's good for you that the check does *not* say "Payment in Full", because such "restrictive endorsements" generally can be enforced in CA - please see the post at the link below.
Disclaimer: This post does not constitute legal advice and does not establish an attorney-client relationship.
I think the lack of the magic words "full and final payment" or "final settlement" or some other words that indicate that cashing the check means that you agree to settle the security deposit dispute means that you CAN cash the check and dispute the amount.
But that doesn't mean you SHOULD dispute the deductions. Judges don't like "gotcha" claims, and I think a Small Claims judge would cut this landlord the little bit of slack needed for being 3 days late in returning the deposit, and for turning down the walk through without noticing or mentioning the burnt countertop until after the 2 days. A burnt countertop is not something you could have fixed anyway, and while you don't mention how much was deducted or expressly acknowledge that you did burn the countertop, ask yourself how your challenge would play to a judge. Run it by some people who will be honest with you, and then decide if you want to bother. Remember that the landlord could countersue you for other damage and other agreement breaches, and if your rental agreement that has an attorney's fee clause, you could also be liable for legal consultation fees (though lawyers aren't allowed to represent anyone in Small Claims court, a consultation can be added to a claim).
Disclaimer: Please note that this answer does not constitute legal advice, and should not be relied on, since each state has different laws, each situation is fact specific, and it is impossible to evaluate a legal problem without a comprehensive consultation and review of all the facts and documents at issue. This answer does not create an attorney-client relationship.