To start with, the early Ford gear sets are bevel cut gears. These offer more resistance than the spiral-bevel gear set in the GM rears.
The 1/4 mile racers could see this on their dyno tests. They combated this by fitting GM gears to the the Ford differential carriers. (very costly) Later, aftermarket gear companies provided spiral-bevel gears to fit.
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^ spiral bevel gears
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This shows the difference well. The automotive gear sets are really spiral bevel hypoid. This means the pinion gear is set at an angle to the ring gear (driven gear). That allows the pinion to be mounted lower than center on the axle.
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^ Hypoid
The second disadvantage to the Ford 9" is weight. On an integral axle housing, the carrier side bearings are supported by the housing. The removable Ford carrier requires the heavy casing for the side bearing support.
The last item is cost to put the 9" in a GM chassis. However you chose to do it, it is custom. Fabricators working on their own vehicle, this may not be an issue.
To answer your other question, the Dana 44 is much like a 12 bolt GM in strength. Dana 60's are an upgrade for both.