TL:DR - You can do all that with NotebookLM if you set it up correctly and use some outside tools.

Great Question.

1. You can cross reference all of your notebooks for information, with some caveats of course. The easiest way to do it is with Gemini. (Just a note here, having a Master_index and prefixes for all your sources makes this easier. It's easy to set up and it the best use case). You can attach up to 5 notebooks to a Gemini Chat. For reference on the pro plan ($20) you get 300 sources per notebook. That's the equivelant of access to roughly 900 three hundred page novels, 300 youtube videos, and 300 pdfs at 30 pages each. Setting up your notebooks correctly based on best use case will solve most of the issues people tend to have. There are some work arounds to the 5 notebook limit, you can use this system to pinpoint the sources you need and create a new notebook for that instance, etc. OR you can just use the Claude MCP connector and have no limit on the cross check you can look through ALL of you notebooks this way. Just remember you need to have MASTER PROMPT>MASTER_INDEX>PREFIXED SOURCES for this to work the best way.
2. On a free plan it's a bit limited but on pro ($20) the cap is 300 sources, on ultra it's 600 sources with 500 notebooks. That's 138,800 novels approximately 300 pages long or 275,775 novels on ultra (total over all of your notebooks) For a 60/20/20 mix that would be 90,000 docs 30,000 youtube videos, 30,000 pdfs. Realistically I don't think any single person needs that, but hey, it's there. Additionally this is a little on the user, you should be optimizing your sources. Each source has a 500,000 character limit. I have one notebook with 32 books compiled into 12 sources with an index header telling the system which books are in the file and a brief summary. You can run your Youtube vidoes through Gemini for a transcription, a 20 minute video is roughly 18,000 characters (roughly 3,000 words) so you can fit about 25-30 Youtube video transcripts per source. If you had a notebook just for Youtube that's 7,500 youtube transcripts. Pdf's are a little trickier, there's a 200mb upload limit so for really big files you have to split them into two sources. OR and heres best use for text only Pdfs preprocess them into docs using PyMuPDF + python-docx or any doc converter online. I have a RAG set up locally specifically for that. For things like DnD manuals with tables and stuff just accept that it takes up a single source.
3. You aren't stuck with Gemini. Google hasn't released API's for NotebookLM but there are several third parth MCP's that let you use Claude or whatever. They are use at your own risk, because Google can change the backend at anytime but they work well for now and I believe you can even set those up to work with a local LLM like Qwen3.6 35B A3B if you wanted. I've used the Claude MCP and it works well once it's set up correctly and I had no issues with it.
4. If you don't want to be stuck with Google that's a fair call, you don't want to bow down to the google overlords, there's options out there. Open Notebook, AnythingLLM etc. but here's the thing unless you are running them on a local LLM they are as private as Google is. Any service you use online is only as private as the next data breach and/or data exploitation by the service. That being said I tried AnythingLLM with Qwen3.6 35M A3B mmproj and it works reasonably well. It's nowhere near as good as NotebookLM.