Generally speaking the config is not sorted alphabetically. Perhaps some small subsections are, but I don't know of any off the top of my head. However it is the case that config is not output in the same order it is input. Output is dictated by the order in which the config render functions output config lines, and there are many such functions.There are no facilities for enforcing any specific ordering scheme, partially because the current scheme should always work and not result in the behavior you described.

If you're seeing a situation like you described with dependent configuration getting lost, please open an issue on GitHub so we can fix that. That is a bug independent of the ordering of frr.conf. There are also misconfigs you could have made to cause the same behavior, so please be thorough in the bug report.