They are talking about the chat template and not the system prompt. With current gen models, the system prompt is only part of a larger pretext that is passed to the model at the start of the "chat". The models are trained on a specific chat template with things like tool lists, reasoning budget, special feature flags and the "system prompt" formatted in a certain template.
Maybe look into model finetuning/distilation. Unsloth [1] has great guides and provides everything you need to get started on Google Colab for free.
[1] https://unsloth.ai/
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