My tuppence, though probably not even worth that :P

I'd wager that the traditional registered tartans are going to be using the "simple" colour scheme available on Scotweb's designer. They'll be generic colours like "red", "green", and "blue". They're also likely to be the most broadly interpretted by different mills.

You can get broader colours by going to the weavers' palette, which has the common colours the weaver Scotweb uses has on hand. You'll get more complicated colours available, but they may be specific to that mill... in other words if for some reason you have to use a different mill, you may wind up with widely varying colours. I'd guess a different mill would revert these weavers' colours back to simple colours and use what they have available.

If you're really concerned about exacting shades, you can use their Pro option, which lets you set the pantones for the colours. It costs more, but instead of names that are open to interpretation you have actual RGB colour designations. You're more likely to get (almost) exactly the same shade every time, regardless of when or which mill is chosen. But your yarn would pretty much have to be custom dyed for you each and every time.