Following up - I solved the issue by using the DT bookmarklets for Chrome, instead of the clipper extension. There’s one that prompts with the popup (where to save, tags etc), and one that bypasses it, silently saving.
The app comes into focus for the latter, but at least it’s doesn’t require action.
PS. I did notice that some websites dont save well… I dont mean one’s that are single page applications with heavy JS, like say Gmail… but content sites.
This link for example : https://www.zooniverse.org/projects/nora-dot-eisner/planet-hunters-tess
Gives me :
Whether I try to save it as a .webarchive or a .html