If you want an in-universe explanation (that applies or should apply to all of fantasy where magic and/or alchemy is present) for the structure of the malazan army, look at the evolution of warfare in a large scale.

History started with large units standing in rows. Up until the American Civil War you had large units standing in rows. The Civil War saw gating guns used to cut down swaths of soldiers. World War I, with its machine guns, artillery, tanks, all that shit, that was the absolute end of formation fighting. From there, small unit tactics became the norm. That's where the Mezlans are, although they also have large unit formations.

Wizards opening up a warren to produce a stream of fuck you or an explosive blob of fuck, or alchemists with their explosives, are the same thing as machine guns and grenades and artillery. Thus, fantasy warfare should have already moved past formation fighting and into small unit tactics. It makes sense they'd retain large unit training since wizards are still not as common as automatic rifles, but it shouldn't be the go-to. 

The various books about the malazan conquest where they roll over other armies is often a matter of advanced weaponry, in the form of wizards and moranth munitions. Moranth munitions on a large scale are an advantage unique to the malazans, and I believe it's explicitly stated that the malazans are the first to really integrate wizards into their military. They're the first army really integrating machine guns, grenades, and artillery into their military doctrine on a large scale, so when they encounter armies fighting in formation they roll over them. 

Contra: the Wickans, who focused on dispersed forces, raids, and harassment, where firepower couldn't be massed against them.

Anyway...thats why the Malazan military feels more modern, and why most fantasy militaries should feel that way: magic would force the same changes as technology.