Does your client have the source code to the Cry engine itself, or are they using version with a binary/pre-built engine and only game-level source code?
If you have the engine code, you can definitely add in support for an arbitrary number of views, assuming you're ok with D3D11 programming and navigating massive, over-complex code-bases.
If not... then hopefully there is some RTT hack you can use :/
If the client is a non-games business where buying loads of expensive hardware is an option, then running multiple networked versions of the engine may actually be the easiest option... We did this in the past for a military contract - we had to add some extra HUD features, and the easiest option was to add an extra PC which rendered those HUD elements and sent the images over the network to the main PC...
cryengine supports VR rendering, that's multi viewport, thus it has multi viewport support.
The cynical interpretation of that is: it's definately supports one specific case of having two almost identical viewports
On a side note; their preferred VR rendering mode is to use a single viewport, which is then post-processed with a parallax shader to emulate two similar viewports.