In some sense it is a KOMA issue, as KOMA is the one doing the patching. Command hooks are quite nice, but they are no fully safe if catcode changes are involved and personally I try to avoid them for long term code. See e.g. https://github.com/latex3/latex2e/issues/1099
caption package: starred \caption not longer works with KOMA
Well I think we can agree that .: looks bad. From the options in the wiki only redefining locally \autodot gets really rid of the period, and imho this feels a bit odd to redefine a KOMA command like this where there is a key to set the postfix text. I expected numberpostfix={:} to overwrite whatever is already there.
numberpostfix contains hard code autodot
ok Joseph confirmed: \int_set_eq:NN expects two int as argument. Either use \int_set:Nn with \use:c or \tl_use:c, or generate a variant for \int_set:Nn: \cs_generate_variant:Nn \int_set:Nn {Nv} \def\blub{123} \int_set:Nv \l_tmpa_int{blub}
Regarding the int: you should use \int_set:Nn\l_tmpa_int{\use:c{toclevel@##1}}. The eq-version is to assign one int register to the other. (But I will ask Joseph if your use should work too, and perhaps adapt the documentation to make it clearer if not). Regarding bookmark: templates can not safely use \AtBeginDocument{\usepackage{hyperref}}. That errors in a current LaTeX. Try it out. I can change in hyperref the commands to \providecommand. Can you open an issue about it in hyperref so that I do...
Regarding the int: you should use \int_set:Nn\l_tmpa_int{toclevel@##1}. The eq-version is to assign one int register to the other. (But I will ask Joseph if your use should work too, and perhaps adapt the documentation to make it clearer if not). Regarding bookmark: templates can not safely use \AtBeginDocument{\usepackage{hyperref}}. That errors in a current LaTeX. Try it out. I can change in hyperref the commands to \providecommand. Can you open an issue about it in hyperref so that I do not forget...
Unrelated but I wouldn't load bookmark (or any package) in the begindocument hook. Better use begindocument/before.