I'd missed that the consultation ruled out the northerly approach, which I think is a missed opportunity. But if Cambourne station is up by the A428 (ie, at the top of the hill), then it would make sense for the line to join WAML west of the M11 to avoid the cost of a bridge, but as close to it as possible to limit the extra distance. There needs to be a crossing of the A10, presumably somewhere Harston and Hauxton...
Not sure about that Tobbes, to join the WAML just west of the M11 would mean crossing the A10 where you say, but this route would then encounter the disused gravel pits immediately to the east. IIRC the M11 is on a high embankment where it crosses the river and the route of the old Oxford line, but perhaps not high enough to get trains underneath so that will be another hurdle.
As jopsuk has said, "Cambourne into Cambridge will be very interesting when it comes to detailed route choice." The old railway definitely had the best approach from the west, following as it does the line of the Bourn Brook, and threading a new route through the villages to the north looks as though it will involve a lot of earthworks because of the terrain.
Also, there seems little scope for crossing the Shepreth branch to get to the GAML, and I think even talk of a new chord at Shelford is a non-starter, because much of the area is heavily built-up. Hopefully they will however be able to lay four tracks between there and Cambridge South, ideally incorporating some kind of flyover to provide direct access to P7&8, though I can see neither project will want to bear the cost of this.