With auto-advance enabled, the Zoom window relies on a default return height in order to know how far down to move to the next line. With auto-advance disabled, tapping the "New line" icon near the upper right of the Zoom window will also move this far to the next line.
To change this value for a template:
1. From the Library view, tap the Gear icon at the top-right corner > Notebook Templates.
2. Tap Edit in the upper right and then on the template name (where you see three dots).
3. Enter a desired value (in points) in the Height field and tap Save.
Note that this change will only take effect for new notebooks using that template. If you want the new change to apply to the existing template, please change the template to another one and then change back.