Having different voltage potentials as power planes on the same inner layer of a PCB
Creating large copper pours for different supplies is common practice even on two-layer boards. You appear to have a healthy gap between the pours and should not need to worry about creepage at these voltage levels.

If these are high-current areas, you may need to adjust for reduced thermal dissipation on internal layers.

And finally, running the 5V signals over these planes should be fine...if you also have a solid ground plane layer, which I'm not seeing in your image (perhaps you have hidden it for clarity). The ground return path should run as close to the signal paths as you can manage, and an unbroken ground plane is the easiest way to manage that.