Can the "option name" display name be different than the actual "option name"?

[mc12345678]

I see two possibilities:
First, you can create option names with identical names for your different manufacturers - you would just have to keep track of them by option id or sort order. You will get a yellow "warning" message when you do this, but it will allow you to do it.

Second, and probably better, is to create one Color option name and all the different option value choices available from manufacturers, and just add the option values needed for any given manufacturer. The only possible downside to this would be if there are different swatch images for different manufacturers' versions of a common color.

And if there are "different" swatches for the different colors, the manufacturers name could appear in the color as well, at least that way you would always know which value went with which manufacturer. One of the reasons I think glenn expressed concern about the difference in colors is that if you tie a photo/additional image to the value, you may end up with discrepancies. (Depending on how the plugin handles/looks up the photo(s).)

But in answer to your earlier question of how handled, we use the single option name with multiple values to choose from method. Making sense to the customer is important and while at it, hopefully not making things impossible to manage on the site owner(s).