This is a very common need and there are a couple of approaches that are less time-consuming than manual segmentation on individual slices. You can get some tips here and from similar topics on this forum: After threshold-based bone segmentation in CT structure filled with holes
What exactly is “BoneExtension add-on” that you mentioned?
Probably the most automated bone hole filling method that is available for Slicer right now is in SurfaceWrapSolidify extension (Segment Editor - Wrap Solidify effect; Filter method: Deep hull; Output type: Segmentation). Have you tried it?