Let me know if I understand your question...

You want to know if it is better to combine objects (mesh>combine) (the objects remain separate) or unify the objects into a single mesh?

That really depends on a lot of things, the most critical of which would be how close will the camera get to the objects and how long they will be in shot and how well lit they are. If the camera is sufficiently far from combined objects you will not notice the lack of the natural bevel that would exist on a unified part.

Also, components that have their junctions covered may be combined to save the time and effort it would take to combine them.

For close shots unifying objects would have the most realistic appearance. Light will reflect off the junctions of the object and look more natural. However, you need to consider the extra time needed to combine and then route geometry to be able to smooth the objects.

Scale effects alot of this too. For a gigantic 60' tall robot you are not going to notice whether a 2' square gear box is made of of 50 parts just stuffed into each other that would take you 3 minutes to assemble or the same part as a unified mesh that took 3 days to work out the topology.

In your example images above, if you intended to smooth that unified cylinder and box you would need to add support edges and would have to deal with puckering in the corners of the box/cylinder junction or creasing of the cylinder as a result of any support edges that ran the lengthwise.

So it really just depends. The camera distance, model scale, technical requirements, lighting, speed of the object in the scene, time the object will be in shot....

I know it's kind of a "cop out" answer but it's the best I can come up with. If I had unlimited time, don't know how close the camera will ever get to the shot, the geometry is not insanely complex, than I strive to unify and smooth as this will give the best result in all possible situations. But in production it's always a balance of time vs accuracy.

Maybe Jay would have a more meaningful opinion as he works in the film and entertainment industry and is always having to struggle with the time vs accuracy dilemma. So he might have some more structured rules for when to unify vs when to combine.