You are correct.
The main purpose of the HP option on the 12S is to act as an electronic crossover to feed a seperate amp for bass management for the mains.
To avoid this and have the 12S pass the unaltered signal to the second sub is to just not switch the HP on...it switches off.
Best thing for the OP to do is use a splitter on his amp to provide a signal to each sub to set each individually, and not even consider the HP function..in his case, he cant use it for anything.
His mains are going to run full range (double bass) whether he wants them to or not, unless he buys a power amp just for them. That would render his Arcam A25 a preamp then, and I believe he sure doesnt want that !
There is only so much the OP can do with the Arcam A25 in this case, and it ain't much.
But as he states, he already ran a sub and knows this.