Close hole function will work OK most of the times but not for thin holes that is are not planar and simple.
Dynamesh will solve most of those cases but will modify deeply the topology. Only a very high res Dynamesh will keep the thin edges efficiently, that can be decimated later to a minimum size
I don’t think it is the ideal solution because the deep topology change but at least works for some needs. Decimation will do wonders keeping the edges in low res. I rather would like also zremesher being able to do it for geometrical objects as always makes a mess of the hard edges, even using curve frames.

Anybody knows other system to close holes for these type of problems? You can create a perfect curve frame around those holes, but then there is no way to translate it to geometry. We can do it connecting two holes in a wonderful way but not to close a single one. Also insert mesh creates a very nice new geometry connecting the new object to the base but no way to use for this case. It seems that Zbrush has the ability to do it but not tools ready.