None of that has anything to do with the fact that you can't counter with shadows up, but you CAN theoretically counter with Third Eye up. Furthermore, the better the NIN, the less useful Counterstance becomes, but a Seigan-using SAM is always going to have windows where she's vulnerable, making /MNK useful even if she doesn't benefit from Counterstance while TE's active.
I was screwing around a bit with SAM/MNK and it feels like I'm countering a whole bunch without losing Third Eye, but I don't know if that's because of Counterstance or the Zanshin buff. Just occurred to me, though (which shows you how much thought I've been putting into this question): we ought to be able to get an answer pretty easily by just using Third Eye without Seigan and seeing if we get Counterstance counters that don't strip TE.