There are more Mother Boxes than the ones on Earth
Being a billion years old, in all likelihood Mother Boxes are rare and discovered, rather than either extreme of being totally unique or interchangeably fungible. Either of these extremes are inconsistent with the film, but we already have perfectly plausible middle ground of something rare but also not singular. In the realm of artifacts, Wonder Woman's magical swords- the God Killer and Sword of Athena, respectively- are a perfect example. Swords capable of out-performing a normal sword by far... but neither unique nor commonplace. Diana was able to replace the God Killer destroyed in 1918 Wonder Woman (2017) with the Sword of Athena through her archeological pursuits, source, in 2016 Zack Snyder's Justice League (2021).
Evidence that there are more Mother Boxes:
- Steppenwolf doesn't immediately connect the discovery of Mother Boxes with the Defiance (the story of the one world that successfully repelled Darkseid before he was enthroned).
- DeSaad actually "entrusts" Steppenwolf to recover and use the Mother Boxes, despite secretly anticipating his failure; something one wouldn't allow if it meant giving up Apokoliptian access and recovery of the sole Mother Boxes for all time; rather, if they can be replaced (even if at high cost) this is a more reasonable strategy.
- Darkseid similarly brushes past the Mother Boxes and focuses on the Anti-Life Equation; if the Earth-bound Mother Boxes were the only Mother Boxes in existence- the only way for Apokolips to terraform planets for their needs... their priority would have at least been on par.
- Diana's story contains far too much information from the perspective of the Apokoliptians to make sense if this is the first and only encounter with Mother Boxes across the multiverse and if the defenders were dusted on every occasion. Rather, those parts of the story were conveyed to the Earth alliance by the "guardians from the stars"- the Green Lantern Corps- who've encountered and repelled the Apokoliptians before. E.g. "No protectors here, no Lanterns..." If the Apokoliptians could only ever advance on a single front with the sole set of Mother Boxes, they would have been contained and defeated by the Corps long ago. Rather being able to strike on multiple fronts with multiple sets of Boxes, is why the Corp must spread out and commit only a few Lanterns to any front... if it were the sum total of Darkseid's doomsday machine, they would have committed the entire Corp to seize the artifacts and stop Darkseid's spread entirely. They don't do that because there are more Boxes out there.
- DeSaad asks, "My master, now that the Mother Boxes have been destroyed, how will you retrieve your great prize?" This is often misinterpreted as "Now that the Mother Boxes [on Earth] have been destroyed, how will you retrieve your great prize [without being able to use the Earth Boxes to Boom Tube to Earth]?" But such interpretation is clearly flawed because Darkseid's prioritization of the Anti-Life Equation is already set-in-stone and if there was literally no alternative, DeSaad wouldn't even have to ask... he would be readying the armada for Darkseid, wouldn't have to even reply because there'd be no question that they're going after the Anti-Life Equation! The fact that Darkseid replies is clarification and selection between options. So a better read of the exchange might be, "Now that the Mother Boxes [only on Earth] have been destroyed, how will you retrieve your great prize [are you willing to invest more Mother Boxes to boom tube to Earth]?" "[No, let's not use any additional Mother Boxes] Ready the armada. We will use the old ways [instead of Boom Tubes and Mother Boxes; by choice and preference... not because there is no other option]."
- [Extrinsic Evidence] At an event in March 2019- long before the announcement of Zack Snyder's Justice League (2021)- colloquially called "SnyderCon", Zack Snyder reveals in a Post-Justice League timeline, after the League save the Earth from the Unity and destroy the Earth-bound Mother Boxes, Darkseid boom tubes into the Bat Cave to slay Lois Lane (a snapshot of this is depicted in ZSJL). This shows that Darkseid still has the capacity to boom tube via Mother Box after Steppenwolf's defeat and the destruction of the Earth Mother Boxes, clearly leading to the conclusion that there are other Mother Boxes available to the Apokoliptians.