LLMs are not inherently non-deterministic during inference. I don't believe non-determinism implies lack of abstraction. Abstraction is simply hiding detail to manage complexity.
pypdfium2 is a great choice and a solid piece of software!
You might want to look into https://github.com/VikParuchuri/surya as an alternative to tesseract. Yes, it's associated with a commercial company, but as you long as you aren't a company with 5M in ARR or $5M in funding it's free to use.
This is an excellent use case for LLM fine-tuning, purely because of the ease of generating a massive dataset of input / output pairs from public C code