It has something to do with the FOV it seems. At least for my case. I am not using the FOV mod from Nexus though.
For me, when I launch the game the zoom works perfectly fine. Let me explain a bit.
My default key for entering into zoom mode is Left Ctrl and I have set 'E' as my change zoom level key. So in Mako when I press LCtrl it enters into zoom mode. Now if I press LCtrl again it goes into a second level zoom and for third press it comes into Third person mode. Now in this case 'E' has no function. But let's say form third person view I have pressed LCtrl once, so it goes into 1st level of zoom. Now if I press 'E' it will change zoom level from level1>level2>level1>level2 >….. . But it won't exit the zoom. I need to press LCtrl again to exit zoom.
Now what I was doing, in console I was manually setting FOV to 90 or 100 etc by "set SFXGame.SFXCameraMode FOV 90" (I think there are other commands as well to set FOV). It definitely changes the FOV of the game. But it also breaks the Mako zoom functionality(i.e. pressing LCtrl will get you to 1st zoom level and then back into third person view and won't go into the second level zoom).
In game even if you use these FOV commands once, Mako zoom won't work anymore till you restart the game.
So, it might be better to wait for some time to use these tweaks properly.
Hope this is helpful for at least some people.