>Splitting it up would make large, atomic refactorings more difficult.

If you split the code base up into multiple projects, you need some sort of meta project to link them all together if you need to deploy it as a single entity. Doing a meta project isn't exactly easy, so it tends to be better to do a single project if everything is all tightly coupled still.

The project could be split up into smaller modules that are linked via shared common interfaces, but takes more time to maintain.