There were no standards of printing. They were developed by different printers in different countries, etc. I wouldn’t be surprised if there were no numbers at all on original manuscripts. The Torah has no numeration. Whoever printed a book decided if and how to enumerate the text. Some books were arranged by full columns on each page. Many were arranged with four columns, two on the front and two on the back.
The first Hebrew book ever printed was the Commentary of Rashi on the Chumash, in Italy. Only in the second printing, in 1475, did the printer think of dating the printing, (historyofinformation.com: “Abraham Ben Garton issues first dated book, etc.”) something that we consider today obvious to include.
When the Talmud was printed (first 16 tractates printed by Joshua Soncino in 1483; [first complete edition, finished in 1523, by Daniel Bomberg, a non-Jewish printer] (Wikipedia, “Daniel Bomberg”), the decision was made to include not only the text of the Talmud, but also two commentaries: Rashi and Tosafot. Someone decided to deem the cover page as “Alef” (without the letter) and the first page of actual text as page “Beit.”
The publisher of Talmud Yerushalmi was at a later time and someone decided to count page ”Alef” as the first page of text, not counting the title page. In a desire to make it easier to remember, most printers kept the same pagination of the Talmud until it became accepted practice. [I remember seeing a one-volume copy of the Talmud that had only the text of the Talmud and the Rashi commentary, printed in the early 20th century by a newspaper company, iirc, which had different pagination, but it was not accepted and I heard from a Rabbi that it was decried.]
