As its name implies, Chapel Hill is a hill. The usual way for railways to go through hills is in a tunnel.
In my younger and fitter days I used to cycle over Chapel Hill. By Fenland standards, it is a big and steep hill. If you look at the map then you will see that the highest point of Chapel Hill is 61m, but the River Rhee valley nearby is only 14m, a height difference of almost 50m. If I remember rightly the road over Chapel Hill has a 1 in 10 gradient on the Haslingfield side, with gradient warning road signs, and I doubt that the local highway authority has to buy many of those.
The proposal in the previous consultation was for the railway to be at a high elevation with a deep cutting through Chapel Hill and a high embankment/viaduct over the River Rhee valley, allowing the A10 road to pass underneath the railway. This was what became known as the Great Wall of Cambridgeshire, with the local NIMBYs erecting scaffolding towers on farmland to demonstrate how high it would be.
I doubt that I was the only one, but, at the previous consultation, I advocated a railway at lower elevation with a tunnel through Chapel Hill, a much lower viaduct over the River Rhee, and the A10 going over the railway instead of under. This makes for a better railway, especially for freight, and, at the same time, a railway that is much less intrusive in the landscape.
I am delighted that the current proposal does almost exactly as I suggested. What is proposed now is so much better than what was in the previous consultation. The fact that the bats benefit too is incidental, this is a real improvement for the railway and for the locality, though I doubt that the NIMBYs will admit that. For me it demonstrates that the consultation process does help to get a better project, just as it did with Cambridge South station.