Just want to chime in here. This bug has been in Scrivener for years. There’s no way (that I know of) during compile to prevent the stupid blank lines on the top – however, I have conjured this VB macro scripts to fix it. They are located here: Fix Scrivener Longlasting Stupidity · GitHub
The first few lines in the link explain how to enable developer options and add the macros. If you do the line removing, it will take a few seconds (or longer for really long documents) to update.