The command extra_dependencies isn't used. For instance, i have in _output.yml:

bookdown::pdf_book:
  extra_dependencies: [
    enumitem: null
  ]
  template: template.tex

or

bookdown::pdf_book:
  extra_dependencies: [
    "enumitem"
  ]
  template: template.tex

and in CSUniSchoolLabReport.cls:

\setlist{partopsep=0pt, topsep=0pt} % Customize spacing around and inside lists
.

The latter file is references in template.tex:

documentclass[
	a4paper, % Paper size, specify a4paper (A4) or letterpaper (US letter)
	12pt, % Default font size, specify 10pt, 11pt or 12pt
	onecolumn,
	twoside
]{CSUniSchoolLabReport}

.

Compilation ends with the error message:

! Undefined control sequence.
l.34 \setlist
{partopsep=0pt, topsep=0pt} % Customize spacing around and insi...

Error: LaTeX failed to compile physics-spring-pendulum.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See physics-spring-pendulum.log for more info.
Execution halted

Exited with status 1.