I doubled the amount of segments but I still notice some small weirdness when I zoom in see something like this. collapsed part of the stack. is this better?
now the real question would be, why does your mesh have this density at that stage? wouldnt it be simpler to model with the minimum amount of faces now and subdivide later?
No pro here, but this is my 5 cents. Also started with Geosphere. used a cylinder to match the topology right (Right amount of Geo) And Boolean. little clean up and TS.
Made this in 5 min. You should try to find the amount of sides that will makes it easier, here 24 and 16. Then, boolean isn't a bad method, it's the correct method for that kind of stuff.
just out of curiosity....why would you want to BUILD that in the LOW poly? if you are going to that amount of polygonal detail....might as well just model a high poly and leave it at that.
You still have MAJOR pinching going on there, add a high spec material and you will see. You need to double the amount of sides your base cylinder has for that to work.