I think the tables as-is work just fine for the retail campaign...
...Now, if you have a mod/work of fiction that doesn't agree with the retail tables, there's nothing from preventing the author with re-writing the tables to "fix" those old errors. The only question is "are the mods reasonable?" Personally, I think you could do A LOT to the Myrmidon and be well recieved for it. For example, I might nix the Helios capability but instead allow the cairrage of the Cyclops under the grounds that fighter's modular configuration allows for the attachment of bomb launchers... or something... Mind you, that would be a fan campaign only.
Also, the GTB Hydra from Derelict is a good example of doing something like this, although they obviously didn't actually change the D.H. itself.
However, here's an idea: You could release a mod which overrides the retail table data with your "fixed" data. Non-invasive, "if you don't like it, can it," everybody's happy...