I haven't had much luck with ISOGEN splitting ISOs where indicated.
Unfortunately, we haven't had much success in convincing other disciplines and our clients to use them when they'd rather just pay us to mark things up, which we do in Acrobat.
My expectation would be that you'd have to receive the PDFs, construct your model, and then output your nodes and coordinates, feed it back to the CAD file, script it into the model, and then reconstruct the ISO drawings, which may or may not match the pagination and spacing of the ones you were initially sent.
Thus, you're probably not saving time and effort, except maybe to push it onto the piper.
I'm not suggesting it's not do-able, but it requires much more data transfer than what's currently available.