No harm at all, but let's be clear:
If you call it anything with 'The Iridium Throne' in the title, half the potential customers won't know what it is you're selling them. Every gamer I have ever met knows the Traveller default background as 'The Imperium'.
So, to put your question back to you, why confuse them?
Fair enough. But so does every 40K fan I've ever met.
It's a fair question, so heres why I'm thinking along these lines.
By putting a Starburst and an s type scout on the cover, and also having in little letters underneath saying "the original traveller universe", you dispel the confusion for a traveller fan in your average gamestore (or at lest most).
I see what you are saying, but where I am Warhammer 40K is much,much bigger than Traveller and their background is also the Imperium. The potential for confusion is much larger, again just speaking of where I am, other countries might differ. In my local games shop there is easily 20-30 times the space dedicated to Warhammer as there is to roleplaying, and far more customers who buy Warhammer than all roleplaying games combined. Sell a book call "the Imperium" and 95%+ of the customers will think its 40K, not Traveller. The bigger gameshop in Cork is the same thing, very little roleplaying and tons of W40K. Up in Dublin GW have they're own stores so there may be less confusion to worry about.
Heck, when I hear "the Imperium" the first thing I think of is 40K. Traveller is 1/2/3rd Imperium to me. (I play both)
The idea for "Iridium Throne" was just to pick something iconic from Traveller that still sounds a bit mysterious and interesting enough to pick up the book and read the back cover. The Throne was simply the first thing that came to mind. It doesn't have to be the throne, just anything that might sound interesting to potential new blood.
I do see the potential for confusion however,
1) I believe 40K has more fans than Traveller*,
2) Most Traveller fans have heard of 40K and its Imperium*. The reverse is not true, unfortunately.
Perhaps the Iridium Throne would confuse some Traveller fans (but again with a subscript and Iconic art on the cover hopefully not to many). But confusing the larger 40K fanbase hardly seems fair. In such a case I would rather see something like the earlier suggestion of "Traveller;Prime" or even "Traveller;Charted Space" or "Traveler;Imperium".
*The above assumptions are based on personal experience and from numbers of fansites and membership, sales figures and the popularity of Warhammer computer games etc. I have no surveys or anything to go on, but the assumption seems fair.