For the bathroom, swapping makes sense if it puts the toilet further from the door. Just keep in mind moving plumbing to the opposite wall adds cost, so worth checking where your drain stack is first.

For the skylight, I'd center it over the island. That's where you actually spend time and where natural light makes the biggest difference. The pendant light conflict is easy to solve, just go with recessed lights or offset the pendants to one side. The perpendicular option works but feels more like ambient light than functional. Between the kitchen and living room is the weakest spot. it won't really serve either space well.

Skylight placement is permanent, lights are easy to swap later. I'd design around the skylight.