In the vast majority of cases, one can support variation in admin preferences by exposing a configuration parameter. Your downvote example is perfect because Beehaw doesn’t run a customized lemmy codebase. There is a checkbox exposed to lemmy admins that enables/disabled downvotes.
Running a custom-codebase is generally the highest-hassle method of achieving some custom-config goal. The absence of communities around this approach isn’t an accident, the people who develop customizations generally try to work with the upstream unless the devs give them good reason not to.