I don't think the Inquisition does much about chapters going over the 10-company limit beyond watching them closely. The Black Templars defy that limit, although they're spread out between multiple crusades, as had been said, and they're not exactly the shining image of Codex-adherence, either. The Astral Claws also went over the limit, but then they did a whole lot of far-worse stuff to earn the Inquisition's ire, not least of which was seceding from the Imperium. The Exorcists also have two additional scout companies.
The Inquisition has much to do with Astartes Chapters. While these chapters are not bound to follow the Codex (or else we'd only have Ultramarines) it is a unspoken and unwritten law that they are not to exceed a thousand in number. They are fortunate that this does not extend to serfs, servitors, or other personnel or Chapter would be very small indeed.
The reasoning is to prevent Chapters from gaining too much power. The whole point of Guilliman's reforms during The Forging was to destroy the Legions forever and insure that no single man could command thousands of Astartes. In essence, at its core, it also is designed to prevent empire-building which the Inqusition would (in some circles) deem heretical.
The Black Templars are under Inqusitorial investigation constantly. Their only saving grace is that they are constantly crusading, in every direction, and at full throttle for the last 10,000 years or else the Inqusition might have penned the crime to them.
The Astral Claws hid
their expansion very carefully and were, in fact, in contempt of the law by empire-building. Huron had a good reason: bigger chapters mean they can hold the Maelstrom easier (and maybe make his own little empire like the Ultras). That was unacceptable. And they were burned for it.
Also, I think it's the Minotaurs who are the HLoT's personal chapter, not the Space Sharks; the HLoT loosed 'em on the Inceptors and Doom Warriors during the Macharian Heresy.
Thats what I meant. I was testing you ...
But I digress here Slumberday. Let us look at this from a more practical mindset -- why? Why does your chapter need 12 companies (one a extra scout and one scouts on bikes)? Why was the standard 10 companies not sufficient?
Astartes Chapters do not make a habit of going around purposely disobeying Imperial laws, traditions, and standards. The Black Templars are given leeway because of their Second Founding heritage, and the Wolves of Fenris for being one of the original legions. They are the exception to the norm, not the norm and should not be called upon as examples why your DIY Chapter does what it does. The Imperium cannot control the Templars or the Wolves and therefore try to mitigate them by isolating their fanaticism and individualism to themselves strictly.
That said if you want 12 Companies, I am not discouraging you from the idea. I am merely saying that by giving us a good reason why they broke the Codex and why they are willing to run the risk of excommunication for what amounts to three scouts companies instead of one -- you will allow me, the reader, to better understand the character and the truely unique
qualities of it. If not then all I see is a 1300 man chapter and it makes me think you just wanted more marines.