I know it's bandied about re 'fish grow to the size of their containment' and I've always just held my tongue but I've had many fish grow to less than their full stature over all my years of fish keeping. And I've never had negative effects. The fish look and act normal, they just don't grow to full. I'm not talking about putting a goldfish in a 1 gallon bowl, though, I'm talking 4' aquariums. I have right now 3 salt water fish; 2 clowns and a blue tang, all of which I know are half size at best, in a 90 gallon. They're just fine. So I'm not surprised your koi is small. But you also probably don't do as most koi owners do and feed until they bust! I think small size is a byproduct of that behavior as much as space. YMMV
And I've recently gotten into koi (for my pond) and I figure with my similar habits of not overfeeding, these new inhabitants won't approach the worrisome size of 30+ inches. Which is just fine with me as it allows me more fish per gallon! 3 of these were bought as 5" tosai 4 years ago and they're now about 14", which supposedly is what they grow in year 2 of their life!