My theory of it is...Probably an easier sell at whatever the MW versions' class was than what most Megatrons come out as.
Megaplex is a potentially very appealing character for HasTak because it offers them easy option for repainting Megatron- a character who always has a unique design, regardless of what series he's in or what the design actually is.
Problem is Megaplex debuted in Machine Wars, and the next time they had have an excuse to roll him out would have been in RiD.
Only RiD was when Hasbro realized "wait we can just repaint Megatron as Galvatron!"
Then they did that for the next three series that followed and by the time the UT was over Megaplex was an oddity in a mostly forgotten toyline.
I actually think Megaplex could make a lot of sense in Generations today.
G1 Megatron can't really be repainted into anyone else, and with Generations not having any tie-in show all it would take would be a write-up on Instagram from Mark to give Megaplex some backstory.
They repainted the Siege figure to hell and back. Imagine if they'd just leaned into a MW-homaging paint scheme for just one of them, and called it Megaplex.
Might have gotten someone tired of the Siege mould to give it another go.
Plus when you look at Megaplex's colour layout... making him a redeco choice for Megatron could allow them to reintroduce "black helmeted Megatron" into things on a semi-regular basis.