Short answer, you need to define the flags in the Guild file. This is a pain I know.
The next release of Guild will have proper flags support for configuration files. This will include the ability to import flags from config files.
I’m guessing your config values are showing up as scalars because you’re printing them to output using the format <name>: <val>. Guild uses this format by default to detect scalars from output.
You can disable this by setting output-scalars to no or by changing the pattern. See Guild File Cheatsheet for examples.