Efficiency First...

[Stormfury]

It's incredibly frustrating that I didn't get credit for Milestones in my save game PRIOR to 1.0.

I'm surprised that finishing each Stage doesn't check that you have researched tech. I get that maybe you didn't want to allow someone to get credit for this by joining someone else game, but for the Love of God and my sanity, at least show us WHICH milestones are missing. I'm at 39/42 with 43 of 44 achievements. The pace of the game is far to slow early game after unlocking alien tech for me to desire redoing everything. If I knew which ones I was missing I could go back to any of 30 saves and try and complete them again. I've bounced through where I thought it might be missing, no such luck.

[Kage Goomba]

It wouldn't surprise me to venture that the achievement only locks in when you've unlocked them in all in a single play-through. (Post 1.0)

Not combination thereof.

Not much point to the achievement otherwise.

[Maehlice]

I mean, if you're just after the achievement, edit a fresh save (using the SCIM) and fill a bunch of containers with everything you need to unlock all the Milestones and Phases. Then unlock them. Advanced settings disable achievements, but I think just editing your save should be fine.