When as means although, it takes some set pattern:
adjective/adverb + as + clause
d. Cold as/though it was, we went out. ( = Although it was cold, we went out)
e. Tired as/though I was, I went on working.
f. Bravely as/though they fought, they had no chance of winning.
Note that as in those structures can also mean because. The context will tell you if as means because or although.
Tired as she was, I decided not to disturb her. ( = I decided not to disturb her, because she was tired)
In AmE as...as is normally used in this structure.
As cold as it was, we went out.
From Advanced Learner's Dictionary -
(conjunction) in the way in which
They did as I had asked.
Leave the papers as they are.
Your sentence #A
Huge boulders, far too big to be used as they were, were lying throughout the bed of the quarry.
Here they were means they appear or their appearance
So this sentence means Huge boulders were lying throughout the bed of the quarry. Those huge boulders are far too big, and not suitable to be used in the way in which they appear.
Your sentence #2
Straightforward as it may seem, the argument is indefensible.
Straightforward as it may seem follows the same pattern adjective/adverb + as + clause
And so here as means although. This sentence means Although it may seem straightforward, the argument is indefensible.
I believe you have no problem understanding sentence #1 and sentence #B.