It's a bummer that Apple Pencil support isn't better in the iPadOS version of Obsidian.

Rocketbook has some products that promise to help with this here. I've tried them and found them high friction but it might be worth it to you.

There's also the pens that use cameras and special papers like livescribe (I think?) but I didn't love those either.

Take a pic of the pages, extract text.

I just take a photo and let an LLM transcribe it