Although I do like the company tool they setup - its fucking fantastic.
It would be amazing, if they'd let you make what you want and didn't try to limit what you call yourself.
The game is about the Maryland Campaign of 1862 and features just the 4 battles during that campaign. Every single unit of that campaign is available ingame for playing (about 900 regiments), thats why the company tool is limited to those units
War of Rights is going for an authentic approach, so to have units like the 54th MA would be ahistorical, since those units in the company tool are also going to be ingame. The company name, the ranks and all that, you set up in your company tool, are available ingame.
If you add ALL companies/regiments, which fought in the war, it would be an insane amount of work, besides the historical accuracy. I don't want to fight against a 54th MA at Antietam for example.
So as you can see, there is a huge design and historical aspect behind that move, to limit the units to those, who actually fought IN the Maryland Campaign.
Once other campaigns are released, like Gettysburg, Shiloh, Manassas or so.. other units are "unlocked".