Nothing overcomes grades and test scores - where applicable. And things like rigor and tank were applicable.
UC does not require (nor read) letters of recommendation at the time of application . A campus may ask for them later as part of a supplemental review, so be sure to check your email.
The reality is your student, IMHO, will not be admitted to a UC. And that’s ok.
Their record is their record. The UCs are great but so are others. And given your son’s Lds maybe smaller schools equipped to work with him would be better anyway.