Simulate Early, Simulate Often... In Rhino
It is apparent to me that S&S automatically "glues" surfaces together that are actually not part of the same surface. In the attached images, the part is made up of two trays bolted together with two bolts, which are each simulated by an intersecting cylinder where the bolt would be, effectively joining them into one solid. There is, however, a gap of .025 inches between the two trays. As you can see, the S&S analysis treats these trays as though they are bonded together, as thought there is one solid wall down the middle of a single tray. In actuality, there should be a stress-rise region surrounding each "bolt."
Is there a way I can control or adjust this "gluing distance," or is there a distance threshold, above which gluing will not take place?
This distance is controlled implicitly by choosing the resolution. As the number of elements gets larger, their size gets smaller, allowing to resolve smaller and smaller features. To see if your small features are resolved, use "grid display" feature on the settings tab, as shown in this video.
Scan&Solve doesn't "know" about contacts (either tensile or compressive) so the "gluing distance" is a function of resolution. Wherever the displayed grid is connected, so too are the physics. Here's a video introducing the grid display and showing how to use it to diagnose weird behavior: https://www.youtube.com/watch?v=pLJc_SxwQ64
For the time being, it is up to the user to identify when simulation results do not make sense and adjust the simulation setup accordingly. In your case, you might have to simulate the components individually. For the near part, you could apply restraints where the bolts would be. For the far part, you could apply the load where the bolts would be.
Does this make sense?