Plants do help with water quality, but they have their own needs and are helped by regular partial water changes because of the minerals in the new water replacing depleted water.
When I'm starting a new planted aquarium, I make steps to help the gravel be a little "dirty" because it is beneficial to the plants, and doesn't hurt the fish as long as water changes are kept up with. Fish poop, and any bits of plant, and algae that falls into the gravel all eventually become what is called mulm. It is broken down to a brown sludge, and when I am starting a new planted tank I put a thin layer of that stuff on the bottom of the tank, and a sprinkling of peat moss. Don't put much peat moss because to much makes other problems. Then I put my gravel, or other planted tank substrate. You can grow plants in large gravel, but they won't grow well unless the gravel is a bit "dirty". As long as the plants are growing and there isn't to much in the gravel it is not a problem but beneficial.
I try to keep it so the bottom 1/3 to 1/2 is dirty and the rest is clean. This is done by only pressing the gravel vacuum on the surface of the gravel but not digging in. This gets the surface junk and extra mulm out, but leaves the lower layers undisturbed to feed the plants.
If you have an area without plants, then sure dig in the gravel with the vacuum and keep that spot cleaner since it isn't helping a plant to grow.
