Research toggle options such as "Earlier Logistics System" have no effect and are always applied regardless of the mod setting
It looks like most of the settings checks in data-final-fixes check the value returned from settings.startup directly instead of checking the value property
e.g.
if settings.startup["senomorerocketman-earlier-logistics-system"] then
should be
if settings.startup["senomorerocketman-earlier-logistics-system"].value then