An IOU written in a gold plate sure makes no sense. I see what you are saying, the inconvenience comes from the fact that the buyer has to buy some amount of BTC at the same time as he buys a share.
That's why I was making the point that you could have a colored coin representing a single share, a different colored coin representing 10 shares, and another one representing 100 shares (like the different denominations of dollar bills). Assuming you have a proper application layer/UI that can hide this from the user, the need for padding is greatly reduced. My opinion is that the protocol should do the minimum required and remain as simple as possible. If a proper UI can work around this, then it might not be worth complicating the protocol for this. Also, the dust rule may disappear all together one day (it's already been slashed heavily to 540 satoshis), at which point we'll be left with a useless padding parameter. It's easier to add something when you need it than to remove it.
But I am posting here to see how people feel about this, and I see you are on the opinion that satoshi_value and color_value should have a degree of freedom between each other. Thanks for the feedback.