I'll get straight to the point:
I do believe that SCAN are, unfortunately, correct to refuse the RMA under grounds of physical damage.
The reasons being that you're required to inspect and inform of damage as soon as possible in order to help your case.
Obviously, for you, this is made to be a hard task due to being busy, so a "an appropriate period of time" lapsed leaving you in this situation.
I do see where you're coming from in that you're a "high" spender, however, if they bend the rules for one person, then they should bend the rules for others.
Sticking to principles is a must to keep a business running efficiently. Unfortunately this time, you've fallen foul of them. But if you think of how many people must "try it on", after damaging boards. Quite frankly it is scary... If we lived in a world of honesty there would be no issue, but this is the world we live in..
In this case it "looks" like a screwdriver has been dropped during installation, explaining the scratch.
The caps are somewhat harder to explain, were they loose in the box, or purely not present?
If the caps were loose in the box then you have no leg to stand on, as there was evidently a problem from the outset.
However if there was no presence of caps then SCAN seem to be relying on the fact of you being able to spot the missing cap locations and scratch.
Which would be fine if you had had time to try the board soon after delivery, but due to other constraints it forced your hand otherwise, making things vastly more difficult.
My recommendation (as much as it sucks), is to take it on the chin this time, because i doubt it would get anywhere in court.
Try to step back and view it from a bystanders point of view:
Being that there is physical damage to the board which wasn't reported in a "swift manner".
Thusly it is a case of your word against SCAN, with SCAN being able to draw on the fact that there is physical damage which points towards (rightly or wrongly) installation damage.
I would recommend that in the future you try to plan around deliveries in order to create time to test a product to make sure that it functions correctly (I know... Easier said than done.)
(Just my thoughts on how it comes across from a bystander point of view)