The contemporary custom regarding pesuchos and setumos in a sefer Torah
The one type of parsha setuma that both the Rambam and Rosh agree on occurs when the new parsha begins after a 'closed-in' space -- i.e. one which is surrounded by script on both ends. This type of setuma has become the standard in modern sifrei Torah. Likewise, today's pesuchos are written in a way that is acceptable to both opinions; they always start at the beginning of a line after a nine-letter gap at the end of the preceding line.
(ס"ק קסד; ביאורים ומוספים דרשו, 186)