After watching the niners film it looks like the middle of the field is vulnerable against the pass. Reeder, Howard and Jones were all out of position over and over again last week. Shanahan is good at misdirection and PA concepts so that is some what understood. However, there were several plays where PA wasn't involved and Rams defenders were out of position. Take a look for yourself.
So, what is the plan? All three Rams defenders have issues. Reeder tries hard but is poor against the pass and stops moving his feet upon impact. Watch him make the initial hit and then just go for a ride. Howard struggles in zone and sometimes looks like he doesn't know his assignment. Does Jones step into the void and take snaps from the others? Well, he was the one who got burned by Kittle for the redzone TD last week. And he has missed a lot of time late in the season because of injury.
Is this an opportunity for Rapp to slide back into his nickel backer role from the 2019 rookie season? He was really good in that limited role. He rarely missed tackles and didn't have to worry about deep coverage responsibilities which give him trouble.
I don't know that the answer is but this looks like a problem to me.