The Header.tex file uses the finalcompile boolean to determine whether todo notes & section labels are shown... but the value of the variable is only set in dfg.tex after the Header.tex has been input. As such, setting the variable in dfg.tex has no effect on the compiled document.
To fix:
Declare the variable in proposal.sty
Move the \setboolean command to before \input{Header}
https://github.com/hoelzer/dfg/blob/f9af0eb47a95fb74fe262c10eec60ec4040f22be/dfg.tex#L17
The Header.tex file uses the finalcompile boolean to determine whether todo notes & section labels are shown... but the value of the variable is only set in dfg.tex after the Header.tex has been input. As such, setting the variable in dfg.tex has no effect on the compiled document.
To fix: