You can conditionally check off a checkbox in a PDF. Just click the conditionally insert toggle:
... then, use the Expression Editor to create a logical rule for when the checkbox should be checked-off.
Note, the Expression Editor (those three dropdowns) is the tool throughout the App Builder. However, in this instance, on the PDF Template Editor page, the Expression Editor can only accommodate simple expressions that can be composed with no more than three dropdowns. If you want more complex expressions, use an Expression Block (this allows to abstract your complex logical rule into a variable, then you use the simple Expression Editor on the PDF Template Editor to reference that new variable).