About Inhuman!Simmons, Raina said back in season 1 that Inhumans have something specific in their DNA, and that she saw it while checking Skye's blood. Now, Jemma was the one checking blood for Inhuman markers, and while I know they meant markers that appeared after transformation, I think there's also something they can check before it. To sum up, I bet they all had their blood checked for this "marker". Also, I bet Garner and Coulson would have noticed her parents in genealogy register.
Yeah the blood marker thing is a potential discredit to this theory but it doesn’t really work for me as solid because they made a point of how much blood Simmons was taking from Skye and she didn’t seem to see anything wrong with it. She kept taking because she was checking for something unusual which she did not find. They’ve made a point of how Inhumans are “human plus” rather than ‘alien’ per se. I mean it’s possible - Andrew worked for them before he transitioned so the blood work he deleted could have been from before transition - but idk I don’t remember anything else that would indicate they could do that, at least not in the face of the dramatic potential.
Plus, if they could pre-test for Inhuman potential I think the potentiality of that (what they could do / who they could save / what privacy they’d be invading etc) would have come up by now. Perhaps they will bring it up soon and we will have the extent of their ability to predict Inhumanity explained?
On the genealogy front: Coulson seems to have sent Jiayings things from Afterlife to Garner - Garner thanks him for sending them, and they seem to me to have been mailed. Also if Coulson (or anyone else) had opened it, he would have been blasted with Terragin dust. Plus, when Garner opened it, he was blasted with Terragin dust. Presumably he got around to reading it later, since he was picking off the names, but a) Simmons’ name wouldn’t be on it because she hasn’t transformed yet and nobody knows she’s inhuman esp not Jiaying and b) the name of whoever might be / have been Inhuman & related to her might not be the name Simmons. It might be further back than that. Jiaying has been alive for hundreds of years - “Thanks to her ability, she was able to guide a number of Inhumans throughout dozens of generations…” (x)
The blood marker thing is a good point and a potential spanner in my works but I don’t think it’s enough to cancel out the possibility given everything else, at least that I can see. It’s pretty subtle without ridiculous levels of analysis and it would only take confirmation of the blood marker thing to shut it down but i don’t think they can do that or I think they would have used it by now.