Sorry, but I've never seen in done in any fan or lighting catalogue. I would suggest that it shouldn't be done

I can't speak to how it will look, but I do know that when you have pendants near a fan, if they are on a cord, as opposed to a rod, they will sway in the breeze the fan creates. Just something to think about. Also, the remodeling forum gets more traffic than lighting so you may want to cross-post.

For the uplight, you could go a few routes, especially with respect to dimming functionality. And some fixtures don't support dimming, so you need to figure that out. To that end, I suggest you think through the use cases. For example, the use case that I think I'd appreciate most is late evening, after you've retired to another room of the house, at which time a mellow indirect glow from the skylight cutout would be particularly pleasant. You might also want the more light from this source on occasion, in which case you'd want brighter lights on a dimmer. That being said, here's some options. I'm thinking two, centered on the skylights, mounted near the bottom rim of the cutout (just above the beam probably). Regarding the pendant, I know that selecting pendants is hard enough without more to think about, but one downside of a single pendant vs multiple pendants is thhat single sources create worse shadows. And the clear glass pendants above exacerbate this harsh shadow problem by being point sources, whereas the Fillsta, for example, mitigates this problem because it's effectively a uniform 31" sphere of light. This large diffuser also makes it possible to use a brighter source. For example, you could put a 300W equivalent CFL in the Fillsta, but such a bright light would be unacceptably harsh in a point source like the clear glass pendants above.

Why not have someone repair the drywall on the ceiling instead, and then the electrician can hang it in the right spot without any medallion. The electrician gave you that suggestion because that is what he could hang, not what can be done.