I am not at all sure I follow what you a trying to do. But to get a bfbs binary schema from a text fbs schema at runtime without calling the flatc compiler, there are probably two options:
One is to figure out what flatc is doing internally and extract parts of the source - it has been done before with the schema parser.
The other is to use libflatcc (I wrote), which takes in in-memory text buffer and generates either C generated code, or a .bfbs schema file.
This example tests a very convoluted fbs schema in memory. You will have to set different options to produce .bfbs files, and it hasn't been tested, but it is designed to support such scenarios.