In a properly formatted manuscript, the first 13 lines are all that the editor will see on the first page.The purpose of those first 13 lines is to get the editor to go to the next page.
Yes, I cut anything that goes outside of the reply box (allowing for spaces between paragraphs if there are any) because the reply box is sized to hold exactly 13 lines of 12-point courier font (manuscript format) text.
Actually, if there is only a word or two on the 14th line that completes a sentence, I will usually not cut that.
A goodly percentage of the "13 lines" that I cut down are probably formatted with Times New Roman font, and while they appear to the author to be only 13 lines, if they were formatted in 12-point courier, they would be longer than 13 lines.
We use the size of the reply box to make it fair for everyone, no matter how they have formatted their manuscripts.
I hope this helps.