I tried the web demo (https://repomix.com/) and it seems to generate unnecessarily complex "packs" for no reason, probably hurts LLM performance too. Why is there "Usage Guidelines" and "File Format" explanations in this, when it's supposed to just be the code "packed"? Better to just have the contents+filename, it'll infer that its directory structure and everything else.
While possibly being strange defaults, both of those are options. Remove the file summary and directory structure, both featured on the UI, and on the CLI tool, and voila, it's in your "better" state. There are also additional compression options beyond those two tweaks.