I would agree, keep clean to reduce scratches, use the clear-bra style stuff to prevent them.
But don't sand down the rubber! Use some 303 or silicone spray to keep it supple. Many times these seals are dirty, even after you may think they are cleaned. If you lay on your back under the door and look up, you can see these seals can be quite complex in form, and you have to use both hands to bend and get cleaning utensils all the way up there. Then, you have to rinse thoroughly! Even on my truck (simple seals) I have to put a good effort into it to get them properly clean.
Also, getting close to the floor you can look into the door as it closes and confirm the seal is rubbing. If it is not, then it is your clothes/shoes.
To get the scratches out, M105 by hand on a foam applicator pad + lots of elbow grease. M105 works surprisingly fast by hand. Follow up with M205 if you want, or just apply some Klasse AIO. During routine washes, a good mist with something like Meg's Ultimate Quick Wax works great, and keeps things clean and smooth.