The payment is late, so yes the IRS and CA can charge penalties and interest. The tax program will not compute these, so your choice is to pay what's indicated and let the tax authorities bill you or you can include something extra but all that will do is lower the interest portion of the penalty.
If you have a reasonable cause (that's a determination made by the tax authorities based on what you submit in writing as the reason for omission from the original return and also being 2 years late in amending) then the penalties can be abated but not the interest.
