Reproducible example: https://play.golang.org/p/uugW5Adb3-J

In the example, the decodeInt function implements a value decoder for int32 that reads an int32 from the ValueReader and multiplies it by -1 before setting it in the struct. The expected output from the main function is

{"int": {"$numberInt":"1"}}

but the actual output is

{"int": {"$numberInt":"1"}}

When using MarshalWithRegistry followed by UnmarshalWithRegistry, everything works as expected. When using Marshal followed by UnmarshalWithRegistry, the custom decoder is not honored.