No, you're right, if you get the car WIM'd, then you lower it, the geometry will be altered so will need recovering again by WIM.
Where I was coming from really was (just IMHO of course) if you were going to do these things separately over a period of time, what I think gives the most benefit etc. So if you were going to do springs and WIM together pretty soon, then that would be good. Although I think that if you put on uprated ARBs and got WIM'd you'd see an even bigger difference (putting uprated ARBs on might upset the geometry just slightly, but nothing like as much as lowering the car).
Depends on whether you were going to get a whole bunch of things at once, or whatever. ARBs cost more than lowering springs though, so it's all a bit tricky doing the whole cost/benefit analysis ! :D
If you were doing all three things separately over a period of time, I still think that the order that I put would be a good way to go about things, albeit with a re-WIM'ing being required with the springs.