Wouldn't they just be able to get around any issues by saying that it's been 100s of years later, so of course machines have been rebuilt? Regardless of your choice, different species would have created and crafted machines after a few years. You could even recreate Geth, as they're a programmed grouping.
As for the green glow, that seems to be something that could easily be a modified choice. It might even be like Mass Effect 2 asking what you chose at the end of Mass Effect. Either it flips every characters eyes green or not. I don't think they'll be too deep with the previous game choices, only slight influence.
Though wouldn't it be impossible to have a Synthesis ending and then have a problem or conflict in a later game? Wouldn't everyone be aware, and almost shared in mind (including machines, meaning they couldn't even go rogue)? Wouldn't it be paradoxical to have choices outside the synthesized group? Doesn't that mean that destroy is the only possible canonical choice, as it allows everyone to celebrate the victory over the Reapers, while slowly beginning to distrust and attack other species over time, in a quest for universal domination, as the Reapers warned Shepard that would occur.
Maybe that's the twist. Control is the true ending, and at the end of this new series Reaper Shepard comes back with the other Reapers and kills everybody because peace didn't last and no one was worth saving.