Oy, what a can of (holy) worms! The Zohar is comprised of many sub-structures which are woven throughout the printed texts. Here's a list of the main sections, aside from the core material (which is called Zohar in the printed text): Ra'aya Mehemna, Sifra D'Tzinyuta, Sitrei Torah, Midrash HaNe'elam, Idra Rabba and Idra Zuta, Raza d'Razin, Tosefta, and there are others. That's not even getting into the question of Tikkunei Zohar, nor of Zohar Chadash. Each of the sections can appear in place of Zohar, along side Zohar, or sometimes, even three sections on a page! And: the standard printed text has not-infrequent textual variants embedded in the text, plus, of course, different editions can vary from one another. I would suggest paginating the Sefaria Zohar like the standard edition (well, "standard" until Matok Midvash and the Sulam editions - hey, that's an idea, get ,Madonna to sponsor the Sefaria Zohar; after all, she paid for the distribution of Kabbalah Center editions of the Sulam for free to residents of Yesha a few years back!). Then, on each page, you could have automatic tiled windows pop up: usually, one window for Zohar, but others would be below/aside it where mirroring the printed text requires.
Or better still: just ask Rabbi Shimon how he wants it presented!

Rav Berachot,
Yehoshua Kahan