No, it's because they see things as either/or that they don't want a via Cambourne route.
They also say that direct St Neots-Cambridge service should exist, but shouldn't be heavy rail as heavy rail doesn't serve all the villages in between. It's classic false dichotomy thinking - that there can only be one service between two places, so either you have fast heavy rail, or local light rail, but you can't have both.
Where they are convincing about not serving Cambourne with E-W Rail is when they say "because we're going to Cambourne, but aren't going to Bassingbourn, serving the latter is a good idea".
I'm not sure it's a false dichotomy, you could have Cambourne served by heavy rail and metro, but it might cause a drop in the cost/benefit of both, and the document suggests that since the commuters from Cambourne are mostly headed to the West Cambridge site and Science Park, so using heavy rail to Cambridge Central, then another mode from there would make public transport less appealing.
I think they have a point, EWR is meant to be a long distance route, not a local commuter route. Serve Bassingbourn, since you can hopefully get money from the developers for the project, and people who want to live in Bassingbourn are more likely to work in the south of Cambridge, so a rail link to Cambridge South(Addenbrookes Hospital) is more attractive.
Cambourne already exists, and once the A428 is upgraded is on a fast road to the West, and hopefully if a metro system is built, they would have a single mode public transport link to the areas of Cambridge they most want to get to.
I personally am in favour of route A, although I do understand people who want Bedford Central on the route. But I think Cambourne is not the best use of the project.