Custom Coders are ignored sometimes

Custom coders are not used when an object is created inside a function that is passed in. It does work in lambdas, I am very confused.

Here is a gist to reproduce it

https://gist.github.com/firemuzzy/d3ed68247a2c0841057fca9864d41fe4

I don't think I have completely narrowed it down because having multiple files also seems to change things. Overall I can't reliably get Beam to pick up my custom coders, I am defining something wrong?