Also, if your combat units are battalion sized, the cost of a command unit with 5-6k command capability is negligible. Its another thing if your base unit is brigade-sized and the command unit needs to control 25-30k.
If you want to get technical about it, the cost of the command unit as a relative fraction of the cost for a base formation is basically constant (neglecting armor, base unit class, capability modifiers, etc.) up to 50,000 tons, since the cost of a HQ unit is still linearly proportional to the command capacity. If you have ten 5,000-ton battalions with HQ5 units, the total cost of command elements will be the same as if you had one 50,000-ton division with a HQ50 unit.
The excessive cost of HQ elements comes from two mechanics. First, and more obvious, is superior command HQs. If you have, say 3x 25,000-ton brigades and a divisional HQ able to control 100,000 tons, the cost of that divisional HQ is a significant premium, and you pay that premium once more for every higher level of your command hierarchy. Second, the size of a HQ component is limited to 250 tons (added, of course, to the size of the base unit class and any other components that might be mounted, e.g., VEH+HQ+FFD), but the cost scales with command capability, which means that the cost of a high-capacity HQ makes up a very large, even dominant proportion of whatever formation it is part of.