Noise on the repellents is just a simple rand() running over the repellent sphere. To change it you just need to modify the @noise attribute in /whitewatersolver/emit_repellants/set_attributes.
You can. But you need to make sure that Houdini actually exports the line to Mantra, by adding it to the "Force Objects" parameter, but you also need to disable visibility by leaving the "Render Visibility" parameter on the object node blank.
The Ocean Spectrum will expect special attributes if you want to go this way. To drive the Amplitude by hand you need to disable the Amplitude parameter on the Ocean Spectrum and create the @amplitude attribute on your scattered points. Or you can instead modify the @amplitude attribute created by the Ocean Spectrum before it goes to the Ocean Evaluate.
Probably because primitive spheres are already a single primitive, so packing them is causing some janky interactions. There's no benefit to packing primitive spheres.