Ok, to start with, all my experience in automotive is working on my own cars; no experience in design, whether parts or tooling of any kind, so I don't know any of the rules or conventions there. I'll mention that I have used Delmia a bit for simulation work, but that's been outside the realm of deliverable data, and the working environment is very different.
Having not been an aircraft OEM, I can't say with certainty why they always want the modeling done in aircraft coordinates. But, here are a few points that I speculate. Please note though, that this all applies to assembly tooling, and I have no experience with detail part manufacture tooling (I expect it's probably the same for detail parts).
1) Data sharing and evaluation becomes easier. As the customer, the expectation is that I can create a new product and insert both the tool and the aircraft parts, and everything drops into the exact right location without needing any positioning.
2) Most parts are unique, one-off parts whose design depends on the position and orientation of the aircraft part, which are also commonly unique parts. See point 1 above.
3) The assembly tooling will determine in large part the configuration of the aircraft component, which of course is critical for the quality of the final product. The design model will be used to generate metrology points; the metrology point coordinates are then used to set the tooling. If the model is accidentally moved in CAD even 0.5mm, then your metrology points will be wrong and the tooling will lead to wrongly built parts. See point 1 above.
4) Doing all the work in a common coordinate system (design, metrology, tool setting, buy off) reduces the risk of errors. Again this relates to Point 1; everybody is playing in the same sandbox so to speak.
So I think the bottom line is a risk management issue, with secondary benefits in terms of convenience that the models will all just line up when done correctly. Hope that helps with your understanding.
Cheers
Mark