Basically, the title, do the chunks this mod generates at game load and with the Generate command contain biter bases? Is it just standard chunk generation like when you explore? Or does it only load the specific chunks that will contain resources? none of these are problems I'm just curious how this works.

This does not change map generation, beyond generating more starting tiles using normal/existing rules (without modifying their design/pattern). If they would have had biter bases when you explored them manually, they should be identical to how the mod expands the map.

Besides asking the game to generate a larger starting area, it has no impact on chunks.

After starting a new game, the mod only reads newly generated chunks for resources, and if found, tags them.

It cannot tell before a chunk is generated if it will have a resource or not. It is designed to look at a chunk the tick after it was generated to see what the game added, and tag accordingly.

Most of the behavior can be found in Resource-Marker / control.lua if you are interested in diving into the deep end. 👩‍💻

Hope that answers your questions -- have fun! 😀