Wait. We must be using the same terms for different things.
By “the Android app” I meant the official app https://play.google.com/store/apps/details?id=io.dynalist
By “bookmark” I meant the dynalist bookmark pane 
Now I see by bookmark, you meant Chrome “add to home screen” icons for tabs zoomed into certain nodes.
I don’t think there is a way to open the app directly to a node.
The app hijacks dynalist.io links in the app (which is an .apk running electron.js and chrome engine), rather than using a real dynalist:// handler in the OS itself. I don’t understand more than that. See here Open Dynalist links in the desktop application (not in a browser!) - #2 by Erica Maybe make a feature request. It seems maybe possible? But might be low on the list of requests Open app and pass parameters with deep linking using Electron (macOS) - Stack Overflow