This is right up my alley. It is likely the scratch is ONLY in the soft clad (almost pure aluminum) finish which is a few thousands thick.... tDrag your finger nail at right angle to the scratch. Does it catch? If you feel nothing, it's not a scratch... If your finger nail catches or feels rough, you want to BLEND it out so you can NOT feel or see it by REMOVING MINIMUM MATERIAL... There are a few ways to blend, but I'd start with a medium scotch brite pad. Work no more than an 1/2 inch either side. The finish will be dull and you should not feel or see any ridge. It may only take a very light swipe of the pad with light pressure to remove the scratch or ridge... WHY? A sharp scratch (even if just in clad) is a stress concentration and can be a crack starter over a long time... however if the stress is low it will likely never crack even with a scratch. High stress parts need more care and attention.
I am assuming the scratch is superficial. With deeper scratches or gouge on thick parts (not sheet metal) you can blend 20 to 1. Say the part is 0.125 thick with a 0.010 deep scratch. You would blend 20 x 0.010 or about 0.20. The total area, size of the blend length and width is also a factor. You can blend more than 10% but requires more knowlege of the part. So if this is 0.040 you would be limited to only 0.004 (4 thousands of an inch). That would slightly be into the base alloy under the clad. It is best to ask Van's if the blend is OK. The know how stressed that area is. You should have some etching and alodine solution and epoxy primer to touch up where you blended. Self etching primer is fine, what ever you have....
Keep in mind the clad is only a few thousands thick and has little strength compared to the alloy it covers... You are not losing strength when clad is blended, but you are removing corrosion protection. Corrosion protection however by clad alone is NOT what commercial makers of planes do. They always etch, alodine and prime, even clad aluminum. This does add weight, and on experimental aircraft you can do as you like. Just be sure to touch up those bare scratches. If you don't want a spot primer job you can prime the whole part. Of course extrusion angles are not clad and should be primed as Vans instructions say, This will restore the finish to prevent corrosion. Clad is for the purpose of corrosion protection because pure aluminum is corrosion resistant more than alloys like 2024-T3 alloy the clad is covering...