I found an issue when Krastorio is also installed. (Though unrelated to that particular mod.)
xmutil.clone() i assume copies a complete prototype including any changes already made to it. Which in this case includes next_upgrade. As for solar-panel-2 (and probably others) the collision_box is changed after the clone, the next_upgrade that krastorio adds to solar-panel (the original) is no longer compatible in size with solar-panel-2. And ofc conceptulally it's not very likely that you want your copied entity to have the same next_upgrade anyway.
And as your forked repository has no "Issues" page... i'm not sure where to report.
