I would suggest keeping those. Settlements in the same administrative units still have their own separate official boundaries (this is even directly mentioned in the ordinance I linked above).

They also have separate addresses and street names (I plan to add some of these in the future) - for example, different sections of შ-208 road are registered as different streets in Nigoiti (Aghmashenebeli str), Cholobargi (Rustaveli str), Chkonagora (Pirtskhalaishvili str), Kviani (Tsuladze str) and Japana (Guria str); despite the fact that they are all part of the same Nigoiti administrative unit.

Additionally, municipal governments sometimes introduce separate regulations/policies/services to separate settlements in the same administrative units. For example village of Grigoleti has an official status of a resort, despite being officially included in Supsa administrative unit with other settlements. (Grigoleti is currently marked on the map with level 8 borders; however this is incorrect [I haven't gone to that section of the map yet]).

As far that I'm aware all the other rural municipalities in Georgia are structured this way: municipalities consisting of administrative units, which in turn are made up of one or multiple settlements (depending on population, geography and/or history). 