Is the cap of sub-units going to be permanent? If it's not possible to do it so it'd be more down to the players choice, that's fine, but it really hits at how flexibly the armies can be made
The limit was actually imposed purely graphically to avoid ugly scroll bars or tricky interfaces. Strictly speaking, you can have more than 10 subunits for any given unit, it just won't show beyond 10 and as such they're inaccessible in that particular menu.
Generally speaking we figured that 10 subunits and 10 soldiers maximums would still allow for infinitely large and complex armies, they might just need to be broken up further.
Say you want a space marine chapter with 10,000 marines in it. Well you could split that up into 10 batallions, each batallion has 10 companies, each company has 100 marines, etc. It gets trickier when you want specific nubmers - ie this chapter wants exactly 17 companies and no more, no less - well in that case it might be reasonable to have 8 main companies, each of which is "1st & 2nd", "3rd & 4th" and so on, containing two subunits that is each a company.
Ultimately the engine can handle near-infinite numbers depending on how slowly you want to play and how powerful your machine is, but it's difficult to elegantly display such compositions in a way that doesn't require each and every game to have a custom-designed layout.
The four additional top-level subunits were added to facilitate support staff for the larger unit (so in this case a chapter). The boxes are smaller, and less visually appealing, but we felt it was important to allow for non-combat subunits of the top-level unit that can be filled with medica, technicians, priests, and so on. These would obviously represent the Reclusium, Apothecarion, Librarium and Forge for a chapter, but could just as easily be a mage corps or stealth teams or similar for other games.
Hope that clears things up a bit