Mesh merging with Slic3r

I frequently have to print a range of different parts each with different geometrical features. So far, I generate each part's optimum printing parameters manually. To be able to print such parts more efficiently, I am planning to create a "library" of individual geometries, each with its unique set of optimum printing parameters. For example, the library would include a 'cylinder', with its associated printing parameters that I have found to give the best surface finish in the shortest printing time.

The issue I am facing here is in combining all the different geometrical features when slicing. (The geometrical features are individual STL files of different geometries). Slic3r does not seem to merge the meshes of adjoining or overlapping solids, making the joints between each different STL mechanically weak that can be snapped by hand.

I wonder why such meshing is not possible. I realise that if each solid on the plater is assigned different printing parameters such as layer height or infill pattern/density, merging would not be possible, however if we keep such incompatible parameters constant for all solids, and only vary, say, printing speed and the number of perimeter shells, merging should still be possible.

Do you feel my assumption above is correct? And if so, is the only way to enable meshing of different STLs into a single solid by modifying the code of the slicer?

Thanks for taking time to read this issue

If you are having the problem with your mesh, then I suggest you repair it automatically using a repair service. I would recommend you try MakePrintable. It fixes nonmanifold surfaces, intersections and flipped faces, wall thickness. It can also and hollow out your models.