I can only address the UC’s and Cal states.
UCB is the only UC currently that accepts LOR’s and they have been by invitation only after the UC application is submitted.
UC’s and Cal states do not require transcripts to be sent with the application but you need an unofficial transcript to ensure all courses/grades are inputted correctly into the UC application.
No GC recommendations needed for the UC’s or Cal states.
Cal Poly SLO admits by major so if he is interested in Physics, then that is the major he should select on the application.  Alternate majors are rarely considered.
Physics at the UC’s is usually found in the College of Letters and Sciences which does not admit by major.  Some UC’s also consider alternate majors so he can select 2 areas of interest on the application.
Below is how the UC’s admit in general:
UC admission by major:
UCB:
Division (L&S, CNR, CoC, CED, CoE) matters for admission selectivity.
Within CoE (but not the other divisions), major matters for admission           selectivity. Changing majors within the CoE after enrolling is not              guaranteed, unless one is CoE undeclared.
    Note that L&S admits students as undeclared; admission to capped            majors (e.g. CS, economics, psychology, ORMS, statistics, art practice,         and a few others) is by college GPA in prerequisite courses (and                portfolio for art practice) after attending for a few semesters.
    The business major is in a separate division and admits students in a       competitive holistic process. Frosh intending business majors begin in      another division (usually L&S), take the business major prerequisites,      and apply (usually in their second years). They also need to take               prerequisites for a backup major in case they are not admitted to the       business major.
All students who apply to UC Berkeley and select a major within the             College of Natural Resources are evaluated based on their application,      not on the particular major they select.
Alternate majors not considered.
UCD:
Admission decisions are made based upon the qualifications of the           applicant pool and the number of available spaces within each academic  area:
• College of Agricultural and Environmental Sciences admits by college
• College of Biological Sciences admits by college
• College of Letters and Science admits by division within the college
• (Humanities, Arts and Cultural Studies; Mathematics and Physical            Sciences; Social Sciences)
• College of Engineering admits by academic department
Students applying as “undeclared” or “undeclared/exploratory” are           considered within the college/division to which they applied.
Applicants are encouraged to list an alternate major, but not in the
same area as the primary major (e.g., Computer Science Engineering with alternate Computer Science in the College of L&S). Occasionally, we admit to the alternate major.
UCI:
- Freshman Selection:
 UCI admits into the University first and then into the major. In the case that  UCI is unable to accommodate all qualified applicants in their first-choice     major, those students who indicate a valid alternate major may be offered   admission in that major or Undeclared.
UCLA:
For the College of Letters and Science, the applicant’s major is not            considered during the review process.
The Henry Samueli School of             Engineering and Applied Science admits students by declared major, with     more emphasis on science and math programs.
The School of Nursing also  places more emphasis on science and math programs and requires the      submission of an additional supplemental application.
The School of the       Arts and Architecture; Herb Alpert School of Music; and the School of       Theater, Film and Television admit students by declared major (within the    school), and put more emphasis on special talents through a review of      portfolios and/or auditions, which are the most significant admission           factors for these schools.
UCLA only guarantees review of an applicant’s first-choice major.
We typically do not admit to the alternate major
UCSD:
The campus does not admit students on the basis of academic major or        choice of UC San Diego undergraduate college. Alternate majors are          considered and capped majors are highly competitive. Also note: Capped majors require additional pre-req courses and specific GPA to be able to qualify if changing majors.  Also if applying to a capped major, select an non-capped major as an alternate.
UCSB:
College of Letters and Sciences: Choice of major is not considered in           selection to the College of Letters and Science. The exceptions to this rule    are dance and music performance majors. Both majors require                 applicants to complete an audition in late January or early February.
College of Engineering: Students are selected by major for all engineering  and computer science majors. Only applicants with a solid background in     advanced high school mathematics will be considered for admission to        engineering. This includes high grades in all math courses through grade 11     and enrollment in pre-calculus or higher in grade 12. A student not selected    for their first choice major will be reviewed for admission to an alternate         major outside of the College of Engineering if one was selected.
College of Creative Studies:
Applicants to the College of Creative Studies submit a supplementary        application in addition to the general UC Application, which is reviewed by     Creative Studies faculty. Students are selected within Creative Studies         majors only. Applicants not selected for Creative Studies will automatically    be considered for admission to the College of Letters and Science.
UCSC:
Important Note for Prospective Engineering Students: Choice of major does   not influence the selection of first-year students, except for those            applicants interested in a major offered by the Jack Baskin School of       Engineering (BSOE). Freshmen who are interested in a BSOE program       should be sure to indicate a BSOE proposed major. Students who do not       indicate a BSOE program or who apply as undeclared might not be able to     pursue a BSOE program.
UCR:
Admission by major but alternate/2nd choice major will be considered if applicant does not need their first choice admission standards.