Well, you could make the main bearing axis the starting point, or a point in space somewhere. The problem comes when assembly constraints start pushing things around. Assembly constraints are among the most glitchy in CAD programs. The tooling plate is not a bad place to start, as the engine has a lot of closed mechanical loops.What the heck are you talking about!?
Another reason is the individual parts can become overwhelming. Having assemblies blocked out helps visualize design intent for the smaller pieces. It also validates the hand-drawn dimensions. He probably got cursed a lot before writing a disclaimer that the project is for experienced builders. There's a likelyhood that if all the parts were sent out to a machine shop as drawn, the engine would not assemble and run.
Along with software issues, I also borrow some of my ideas from ASME Y14.5, where:
Datum features are selected to meet design requirements. When selecting datum features, the designer should consider the following characteristics:
Readily accessible surfaces
Surfaces of sufficient size to allow repeatable measurements
I mean, I wasn't totally being altruistic. I made the instructions for meselfish too.