The metaphor of wearing a belt AND suspenders springs to mind.
I am not an FM3 knowledge demigod but in many cases people have cab blocks in their presets. To mic the CLR would be, in a sense, to mic a cab that is putting out the sound of a mic'd cab already. Even with an FRFR the mic itself will introduce some coloration and characteristics of its own. Beyond that, mic'ing cabs or amps has always been a fussy pain in the backside in studio or onstage. Working out mic placement, fiddling with a stand or hanging a mic over the top of the amp and taping it in place etc. Then there are the considerations of room size/shape/acoustics, optimal stage volume etc. One of the FM3 (or other modeler)'s selling points to me was the ability to eliminate these considerations and compromises in one go - with the bonus of the output sounding the same or very similar through studio speakers, a PA, a FRFR, headphones, a wedge etc. Instead of the guitarist having to plan for every contingency and buying, packing and transporting the gear (mics, stands, cables, adapters, tape) there is a consistent method of amplification and connection and it involves minimal time and manpower. It's like stealing.
I just looked at the CLR...it's a nice unit but ouch! That price tag. 33 lbs is a nice manageable weight though.
Not to brag - OK I'm bragging - but I went ahead and sought out the GR Guitar powered cab. 2x10 stereo, 600W (!) and...18 lbs thanks to the carbon fiber shell. And thanks to the forumite who first mentioned the GR brand - but finding a unit was devilishly difficult. And not cheap either.
To answer the question - although others have answered it already - I would go with option 1. It would have been very easy for Fractal to issue the 'basic' FM3 with only one set of outputs with one level control and drop the monitoring issue in the lap of the end-user who would have had to rely on the sound man or some separate piece(s) of kit. Having two sets of outputs and two level controls covers the FOH and the stage situations and gives the guitarist the ability to 'mix himself' onstage without the sound man knowing or even caring. So why not take advantage?
(Editorial aside: I have two rare gripes about the FM3's level knobs. They turn easily - too easily - and therefore may often be knocked out of desired or set position especially in a live situation where mix is critical. They are also rather small and flimsy in my view. Due to the dimensions and shape of the unit especially when stored/transported having taller knobs might be impractical as they would be damaged or even knocked off. But larger knobs about the size of vintage Fender amp knobs or those found on a variety of pedals might work better. And harder-to-turn pots under the knobs might help guard against accidental or unwanted movement.)
It is possible and very common to daisy-chain XLR cables if a longer run is needed. Gear and sound anoraks will debate you until your eyes cross about the merits of this method but in a practical, live setting any drawbacks to this approach are insignificant. As someone elsewhere noted, 'a recording studio might have an XLR run of 200 ft or more. Connecting two 25 ft XLR cables to get a 50 ft cable isn't going to have any noticeable effect on sound.'
