I've never stained or installed a wood floor, but I've stained a lot of other wood and I'd like to share my opinion.
First, the top coat will help protect the actual wood from being scratched. Obviously some scratches make it through the topcoat, but the majority should not.
Secondly, the stain penetrates more than just the very top of the wood. Depending on the grain, I've had some wood take stain over 1/8" deep.
So it would take a very deep scratch to show the raw oak and even those can be touched up as Gary has mentioned.
Hope that helps,
Russell
_________________ Hardwood rookie.
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