The pond with the smallest muck problem is a pond with no water. Silly, but true. We add water because we like the look. People add rocks because they like the look. Rocks are as important, maybe more so, than even water. Based on Aquascape style being the most common type of pond by far.
The question imo should be what amount of muck will you consider acceptable. Wildlife Pond owners love the muck. Koi Pond owners absolutely hate even the smallest amount of muck. Most Water Garden owners are kind of indifferent until there's a big problem.
Adding rocks doesn't increase muck. It does effect muck removal choices. For Aquascape style owners draining and power washing a pond once a year is no big deal for most owners because the pond dude does it. For most Water Garden owners it's no big deal because they never clean the pond.
A bottom drain system can certainly be made to work with loose gravel, rocks or whatever as long as you're OK with the amount of trapped muck. Basically what happens is the gaps between rocks, gravel, fill with muck. Once filled the additional waste products will bounce along the surface and into the drain. The amount of trapped muck you're willing to allow can be adjusted by adjusting rock/gravel size and shape, adding more TPR and/or flow, changing the design of a pond to River Flow, round vs rectangular, etc.
An epoxy surfaced round pond is probably the easiest to keep absolutely clean. Basically a settling tank that flushed 24/7. As you change that design the muck removal requirements also change. Adding rock is only one of many factors that effect this.
I like the look of rocks. I fill the gaps between rocks with mortar. Exactly the same look but no muck. The fish loads I keep are fine with that.