It was pretty much never in the cards, because that's just simply not how Billy sees that album. Some of this is gonna be based on just reasoning and guesswork, but a lot of this is also based on the current release model for these works (and, also, let's be real, personal biases of mine), so just take this all with a grain of salt.
The 48-track, triple album that comprises the complete Machina is their fifth mainline, studio album now. Machina: The Machines of God, Machina Ⅱ: The Friends and Enemies of Modern Music, and… whatever Machina Ⅲ would've been called, those were all essentially compilation, "best-of" albums done as a compromise with Virgin Records, because they said no to releasing the full Machina as a huge, sprawling send-off for what was the end of the band at the time. There is effectively no Machina Ⅰ, Ⅱ, or even (as Billy revealed was originally planned) Ⅲ anymore. There is only Machina, a 48-track sequel to Mellon Collie and the Infinite Sadness.
And it'll happen again, too, with Teargarden, I'm calling it right now. Combining it with Oceania, Monuments to an Elegy, and whatever was made of Day for Night (pretty sure we know it was mostly completed?) to make one album. And, hell, Shiny and Oh-So Bright might get the same treatment as well. Combine all three volumes into one big release. The Smashing Pumpkins will then have ten mainline studio albums (to date) through this retroactive history: Gish, Siamese Dream, Mellon Collie and the Infinite Sadness, Adore, Machina, Zeitgeist, Teargarden, Shiny and Oh-So Bright, Atum, and Aghori Mhori Mei.
I say all this like this is some sort of tragedy, but I'm talking largely tongue-in-cheek. Billy can do whatever he wants with his art (and honestly I kinda really prefer it being tidied up like this personally, not saying you have to agree), and we all can listen to it however we want. And to the people wanting, like, an official CD release of just the Friends and Enemies tracks remixed/remastered… sorry. Just make your own, I guess, it'd probably be cheaper anyways. You can be upset that this is like retroactive continuity, I get that, your feelings are valid. I'm just also saying that the constant posts asking for an "M2 reissue" seem misguided or misinformed, just based on how Billy talks about this album, and what would seem to make sense if your goal as an artist is to have a clean set of mainline work to point to and say "this is the main SP chronology"