Due to the dispersed mass production in WW2 it's probably not totally true that they wouldn't fly without a custom tooling setup (it'd be a maintenance nightmare if two examples of the same model from different plants diverged dramatically, altho of course it happened) but you can be certain that it's of critical importance.
For mass production, they had to be re-tooled with larger tolerances which also allowed for interchangeable parts.
Do you remember where you read that? Sounds like an interesting bit of history.
The analogy to out-of-date software documentation is very apt. As problems or inefficiencies popped up in the factory, they'd change things and just not write them down (because of deadline pressure, often). If you wanted to build new ones you'd have to either get the factory workers to show you how the thing was actually built, or tear down a working example to reverse engineer it. (Which has been done!)
How things came to be and are, are often at times not documented. Dimension and tolerancing is lost over time too.