I now have 2 mutitools. I got the second one much the same way @TravelEcho describes. As far as I remember, when I was offered it, I was given choices by way of click-boxes. It worked much the same way that ships do.
I could choose to accept the new mutitool, in which case it would replace my existing one. Or I could choose to add it to my collection, in which case I got to keep both.
On PC, under the X button menu, there is now a new item that allows you to select from your collection of multitools.