I went to an earlier save and went through the process exactly as described. Same behavior: I can create Mark 2's, and solar reflectors, but the option to update 3x3 marital plots isn't available on the "customize plot" menu. I tried with plots created before the feature was available and after.
Two things to consider: 1) I notice that I don't get the dialogue where Magnusson says he'll put a targeting gun in my quarters 2) I did use the "cheats" menu to unlock all plots, plans, classes, tools, etc. when I first started the game. Could that have something to do with it? Also, am I supposed to wait for him to specifically tell me to do the research? Because I didn't. I did find the targetting gun in the BADFTL. It doesn't work with error "no uplink available"...which makes sense since there's no tower.