So, I tweeted to them a quick question and it turns out they DO accept author manuscripts, but that their instructions are on the fritz right now!
@CancerConnector A single PDF at 1st submission is ok but needs to be changed at revisions. Will contact you by e-mail.
— PLOS Comp Biol (@PLOSCompBiol) April 13, 2015
Anyways, they replied quickly with an email as well stating:
We allow a single PDF to be submitted at initial submission, although as the paper is subsequently revised, we require the manuscript to be submitted in separate parts to begin to prepare the manuscript for production. This is to avoid asking authors to do everything at once at acceptance, a process that can, in some instances, be a substantial task.
I understand that this is not clear on the author instructions and we are looking at ways of improving our instructions.
So - submit away. And, thank for the quick reply to PLoS CB... now it's just fingers crossed for our submission.