Lines in a Sefer Torah

There are various opinions as to how many lines there should be on a regular page of a Sefer Torah and to what they correspond. The Tur (יו"ד סי' ער"ה) brings different customs, stating a range of 48 (corresponding to the journeys of the Jews in the desert) to 60 (corresponding to the 600,000 Jews). He then brings the opinion of R. Yehuda of Barcelona that it should be 42 lines corresponding to the word “בם.”
The principle source for the number of lines is the “small” Mesechta of “Sofrim” which mentions that it should be 42 lines corresponding to the journeys of the Jews in the desert. The source of the Tur who mentions that it should be 48 lines correspondent to the same thing is from a responsa of the Mahara”m of Rothenberg. This begs the question – if the source says 42 lines, and looking in the Torah one will see that this is indeed the case, how could he say that it’s 48 lines/journeys?
It must be that the Mahara”m is including the travels the Jews did in retreat after Aharon's death, which are technically not counted as part of the 42.
פרישה יו"ד סי' ער"ה סקי"ג-י"ד