Which would be stronger or better, having a front differential that is housed in an aluminum case with differential fluid OR being housed inside of a transmission case?
I don't think just because a differential housed in its own case is indicative of its strength or ability to handle power or if its "better."
For example, lets take some moderately powered AWD cars that utilize a transaxle where the front diff and transmission are housed in the same case: WRX STi and Lancer Evo. These cars have their front diffs and tranny in one case and can handle 300+ HP. The FQ440 Evo had 440 HP. Another example would be a Porsche 911 GT3, except now the engine is in back and again the diff and tranny are housed in the same case. The current 991 GT3 with the 4.0 makes 500 HP and 300 something Ft-lbs.
Not a lot of vehicles that come to mind to me at the moment that have all differentials in its own case except for most 4WD trucks and the legendary Acura Legend (pretty sure there are other examples). Trucks have a separate diff for the front more for packaging and weight distribrution reasons than for it being heavy duty. As for the Acura Legend, well... I remember reading somewhere that Honda claimed it would improve handling or something like that. I think they just wanted to look like the other high end european makes and Lexus.
However it is easier to service a diff with a separate case if you just want to only service the diff like switching out gears, use different oils, add a limited slip, etc.
I do agree with you that a vehicle equipped with AWD or 4WD can put more power to the ground and fully utilize it.
One last thing in regards to the diff fluids for the CX-5. Even though the diff fluid may look murky, it doesn't mean that the oil cannot do its job or is harming the differentials. I worked on a Nissan 240SX with a full Sylvia conversion and it had a LSD in back. The owner liked to change his fluids annually he barely put less than 10K miles a year on that thing. And even with the low mileage he was driving, the fluid still looked dirty everytime I changed it. I think it would be interesting to see what an oil analysis would show for the CX-5 diff fluid at 50K miles.
Having said all this, it's your guys' CX-5, if it makes y'all feel better to change it early, then by all means. And its cheap.