Merging units, not way too complex. But giving orders to subsections of a formation consisting of two or more units, yes, that is way too complex. I don't see why you should have to do that, rather than having the merged units make use of their subsections on their own discretion.
It is precisely no more complex than ordering groups of units into a group formation, or ordering a single unit into loose or wedge formation. You click on two or more unit types, and click a button, instead of dragging lines out yourself.

That's what runners were for. Evidence - no, proof - that you're playing as a general: you command ALL your units, not just one, or a few. You can select several units and group them in various battle formations, something which only the general could do. As if that wasn't enough, you're the one who's calling the shots on the strategic map.
Lol, runners are not instant battlefield communication, they could in no way justify the degree of precision you have as supposedly the general of your Total War armies. Calling the shots on the strategic map is even more evidence you are not RPing the general in Total War as generals did not decide construction projects and tax rates. You're playing some kind of spirit in Total War figure basically who can influence all these different individuals in a nation to make different choices. You're definitely not the general, and even if you were, what in the blue blazes stops a general from shouting "spearmen in the front two lines foward, back two face rearwards" or "swordsmen, alternate lines with those archers!" ??