I absolutely agree with @gavinbrooks. Starting out with my PhD I want to keep my handwritten notes & summaries as close as possible to the source PDF and this seems to be a perfect way to do it. Particularly adding blank pages in the PDF could be very helpful to write more comprehensive summaries - as would be possible with Goodnotes. However, if i may cherry-pick, i than would rather use your text marker, that easily spans multiple lines, rather than Goodnotes text marker, which is more of a freehand single line tool.
Another viable alternative in my “Summary case” would be to allow multiple file attachments alongside the source PDF. I imagine having the source PDF open and than switching to a Goodnotes file - where i could insert screenshots of the source into my notes.
Overall, I think the least complicated feature would be to allow inserting blank pages into the source and than use the available tools (+ maybe screenshots? → This way I could annotate or reorganize e.g. graphics and put them into a broader context).