How to handle pricing as a freelance designer

Anyone have any experience/tips on budgeting the CAD portion of a project? Where despite best intentions, the full extent of the 3D problem solving can’t be fully understood until you are elbows-deep in a model?

My example is that I’ve completed the first two flat-rate phases of a project (initial research and scoping, and narrowed-down to two solutions worked out in sketches and AI). I now need to estimate the CAD portion.

My hypothesis is that I still should follow the rationale of the first phases and hope to get ‘close’…its either that or start with an estimate and then bill it hourly with a “not to exceed” fee…which more or less amounts to the same thing.