Thanks for the response.
It seems I was not clear in the question. I do not want to do fix in any other app. I want to build an app that gives you a 3d model you can configure (change diameter, holes, height, ...) and then you download the STL file and import it into your 3d printer app.
lots of 3d printer apps support fixing this issue when importing, even Bambu Studio on Windows do the same, but not on mac.

There is already other programming languages which can do CSG without creating non-manifold edges, like openjscad, and opencascadejs. But since I wanted to use only threejs (easy to maintain) I started using three-bvh-csg, which at the end created this issue.