Hi synaps,
In regards to your question - "Does this mean that even if I meet the 90% requirement but still owe tax after April 15th, I'll be subject to the late payment penalty and interest?" Yes that is correct, but only on the amount still due.
The late payment penalty is calculated at .5% of the unpaid balance per month, beginning April 16, up to 25%. The penalty for late filing is 5% per month, so it is definitely important to file on time even if the taxes aren't paid yet!
The interest is calculated on the balance due, so if you are assessed a penalty and haven't paid it, interest would accrue on that as well.
CA rules are similar to the IRS, here is a link for that information: https://www.ftb.ca.gov/pay/penalties-and-interest/index.html
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