The report is riddled with confusing references - like how the 0.82 BCR of the local service is somehow meant to worsen the 0.14 BCR for Option 3 - good to know they know their maths.
This report would have cost a lot - I fail to see how they couldn't cost Option3 being mostly single-track; surely no-one is expecting it to be the new mainline?? If would be for back-up, and can be used whenever there is planned closures anywhere between Plymouth and Exeter.
Capacity wise, when HSTs are diverted via Dartmoor, I think passing loops to allow 1tph in each direction would be acceptable, surely? I know Plymouth to Exeter is usually 2, but it seems that would be reasonable back-up. In an ideal world, it would be worth spending that extra 20% to double track, seeing as £600-700m is being committed anyway - but if that's the difference between it being viable and non-viable, I'd take that.
The main line has single line sections for certain stretches - even if a predominately double-track line was constructed, surely things like Meldon Viaduct being single-tracked is a no-brainer.
That said, St Budeaux to Bere Alston should be doubled, as the bridges etc are already there, and would allow for delays. Cowley Bridge to either Crediton or Yeoford should be doubled too, for both delays and for capaicity for the Barnstaple service.