We have figured out a solution, in the next Tropy release there will be a way to skip line numbering:
Simply create a horizontal line by typing three dashes (---), Tropy automatically converts the dashes into a horizontal rule which will be excluded from line numbering.
If you prefer spaces over lines please head over to the ‘Customizing Tropy’s UI Styles’ post and have a look at how to hide lines: Customizing Tropy's UI Styles