The problem with the Italians was not that they had binary divisions, but that they had limited amounts of older types of supporting equipment. Lets look at the Italian vs German 1940 infantry divisions, on the basis of support per infantry battalion. The Germans had 9 battalions and the Italians had 8 (6 infantry and 2 CCNN).
The Italians had 1.5 x 100mm howitzers, 3 x 75mm guns & 1 x 65mm infantry gun per battalion while the Germans had 1.33 x 150mm howitzers, 4 x 105mm howitzers, 0.67 x 150mm infantry guns and 2 x 75m infantry guns per battalion, a clear advantage to the Germans in both numbers and quality.
The Italians had 3.75 x 81mm mortars and 15.75 x 45mm mortars while the Germans had 6 x 81mm & 9 x 50mm mortars. The Italians had more mortars altogether, but both fired lighter bombs than the Germans and the 45mm was slow to operate, meaning the Germans again had a significant advantage.
The Italians had all of 1 x 47mm AT gun per battalion while the Germans had 8 x 37mm guns. The 47mm may be slightly better than the 37mm, but not better than 8 of them. The Italians had 7.5 x HMG's of an obsolete design while the Germans had 12 x HMG's per battalion that were unmatched in the world. In terms of specialised HOI4 support units, the Italians had 0.125 engineer, signal and medical companies per battalion while the Germans had 0.444 engineers, 0.222 signal and medical and also had 0.222 recon companies.
Then if you look at the basic infantry weapons, the rifle & LMG, the Germans had the better quality again. Its no wonder that Italian troops performed worse than German troops when pitted against the same opponents.
If the HOI4 combat system is designed properly, and where the weapons/equipment numbers and quality per battalion is equal, it shouldn't matter if an army brings 2 x 9 battalion divisions or 3 x 6 battalion divisions into a fight. The advantage of larger divisions in HOI4 should be that we get more value per medical, logistics, signals, maintenance, engineer and recon companies, thus allowing savings in the production of support equipment, with the downside of less flexibility in that 2 larger divisions can at most do 2 things while 3 smaller divisions could do 3 things. Command limits should be another advantage of having larger divisions, but with Field Marshals having unlimited abilities that doesn't really apply.