I am NOT a medi-cal biller (thank heavens!), but we do see some Medi-Cal patients at an inpatient rehabilitation hospital. I bill for a physician, not the facility.
I was having 90% of my claims denied (the few 10% that were paid were exactly the same as the denied ones but were somehow getting paid). It all had to do with my modifier and my place of service. I did exactly what the manual said, got denied, appealed and was told to do... wait for it... exactly what I was already doing! So I called and they had a regional rep (can't remember their exact title) reach out to me. I emailed her the documents for research. She came up with... NOTHING DIFFERENT!
My scenario was this: place of service 61 (inpatient rehab hospital) is not on the fee schedule and will not be paid without modifier U2 (and that was what was denied). I finally suggested to the rep that I use pos 21 since our hospital was indeed, a hospital. Of course I did this in email, so if I got audited later or Medi-Cal decided they wanted their money back, I would have everything in writing. She agreed that we could try and change our POS. It worked. I just got a big check for a bunch of claims yesterday.
So while I don't have an answer for your scenario, you might have to just send a claim in and see what happens, or think outside the box, OR call them for a rep to call you back.