The ending of DaiFukkatsu is still somewhat of a good ending.While you certainly may not have prevented NEXY from causing the events of dai ou jou without knowing it, at the very least you did stop Longhena and pals from the future from altering the past into an even worse state than it already is.
In the crossover of DaiFukkatsu and Ketsui...As seen in a playthrough video, the incarnation of Evaccaneer DOOM, namely the True Final Boss, is a target of combat simulation prepped by Tiger Schwert's pilots, complete with them contemplating about the machine's existance. However, as they try to make out the name of the machine, it says Hivacaneer Hi-VA-C (pronounced as He-va-see). It strikes a conspiracy overtone in that the head of EVAC and Colonel Longhena are in cahoots
SDOJ Hibachi got the idea for "converting all humans to robots" from LonghenaWho else would want such a thing and it's been said the ending text has her remarking on someone suggesting the notion to her. He likely had a role in breaking her out. Inbachi? Likely a mentality that he created if not a clone.