I am working on a design that is similar shaped to a wine glass, to improve the strength of my connection point betweeen the stem and the base, I’d like to fillet the stem into the base, but I seem to be only able to fillet the base separately and then the post just meets on a flat plane at the center/top.
Make sure the cylinder is actually in contact with the base. It can appear to the eye that it’s touching, but it may be a few hundredths or thousandths of a mm separated. You might consider embedding the bottom of the cylinder in the base to make sure.