Boolean operations VS Merge Distance

Boolean and Merge by Distance are for completely different jobs.

One isn't "better" they solve different problems.

Here's the breakdown:

Tool	What It Does	When to Use It
Boolean (Union)	Creates new geometry where two shapes intersect. It adds connecting faces and welds everything into a single, watertight mesh.	When you have two overlapping shapes and want them to become one seamless object (e.g., merging a cylinder into a cube to make a rounded handle).
Merge by Distance	Only welds vertices that are already touching or very close. It does NOT create new faces or geometry.	When you have two meshes that share the exact same border/edge and just need to be "stitched" together (e.g., joining two halves of a symmetrical model).

Aspect	Boolean (Union)	Merge by Distance
Creates new faces?	Yes — it generates connecting geometry.	No — it only welds existing vertices.
Works on overlapping shapes?	Yes — perfect for intersecting objects.	No — if shapes overlap, it leaves internal faces (messy).
Leaves internal geometry?	No — it cleans up hidden faces automatically.	Yes — overlapping faces remain inside the mesh, causing problems later.
Topology quality	Often messy (triangles/ngons) — needs cleanup.	Usually clean (quads) — if the edges align perfectly.

Imagine you have a cube and a sphere sitting on top of it:

Boolean (Union) → Creates a single object that looks like a cube with a dome on top. The geometry is unified, and hidden internal faces are removed.
Merge by Distance → You press Ctrl + J first, then merge by distance. The sphere and cube are now in one object, but the sphere is still floating on top—no new faces connect them. If you look inside, there's a mess of overlapping geometry.

If you try to use Merge by Distance on overlapping shapes:

The vertices don't touch (because the sphere is sitting on the cube, not sharing edges).
Nothing gets welded.