How can I enter Greek numerals based on obsolete letters {Ϛ΄, Ϟ΄, Ϡ΄}?
Have you checked the Greek Polytonic input source provided by Apple on the option and option-shift levels?  

Otherwise the usual way to enter archaic characters is via the character viewer.

If you need them often, you can make a text replacement entry in system preferences > keyboard > text > replace with.

If Greek Polytonic doesn't have everything you need, you can make a custom layout with Ukelele.