I'm not at all familiar with the MC 16, but for what it's worth... on page 19 of the current CLC catalogue is a picture of a hybrid MC model with a conventional carry handle at the bow.  I gather that your query relates to accommodating the rudder installation at the stern.   On my Ches 17LT, just completed, I have installed a rudder, and my carry handle at the stern is simply a stainless steel saddle - like the one pictured as above - but mounted across the craft rather than along the centreline.   It's exactly 6" in front of the stem and clear of all rudder components and lines.   This enabled me to screw it through the deck and into the sheer clamps underneath, giving maximum strength.  

Saddles are available in various sizes so it would be a simple matter of measuring the across-deck width just in front of the rudder assembly and buying the appropriate size saddle.   I ran my uphaul line through (under) the saddle too, just a minor point.   Alternatively, if you want to use a proprietary carry-handle (such as CLC sells, I believe) you could mount this across the deck too.

A third option is to mount carry-handles on opposite sides of the craft, again screwed into the sheer clamps, bow and stern, which with a canoe's greater width may make carrying easier - one person on each side, bow and stern, with the handle immediately under them instead of in the mid-line of the craft, less awkward and nicely balanced.   With this, the stern handle will be mounted on one side, well clear of the rudder components, I'd think.

Hope this may just assist your planning.

Cheers..

Wordsmith