You mentioned two-tone wood boxes. I am not sure if I've ever found a pre-made wood pen box that was made from more than one kind of wood. Do you have any more specifics about exactly what kind of box you are looking for, and how two different woods would be used together? Are you just thinking one color wood for the base part, and a different for the lid, or are you thinking about something more complex? Perhaps a darker wood for the sides and bottom, lighter wood for the front, back, and top?
Also curious what kind of interior you were thinking about. Simple, say just a routed channel for the pen? Or were you thinking something more elegant? Felt lined or flocked? Any idea on the hardware (hinges, etc.)?
I've been wanting to make pen boxes for a while, so I've thought about potential designs. I actually don't have the tools yet to make them (I have a table saw, that's all, and I guess technically I might be able to do it just with that, but I think I'll also need a planer and a router to really do everything I was interested in.) So, I'm not offering to make any for you. That said, simple boxes can be pretty strait forward, especially if you just want a simple routed channel. That can be as simple as two pieces of wood, same width and length, with a channel routed down the middle of them for the pen. You then just need a couple of hinges and a latch. Such a simple wood box shouldn't be hard to make, if you have the necessary machines (table saw and router table.)
More complex boxes would probably also need a planer, or perhaps a thin-rip jig for a table saw. You would then want to consider how to actually assemble the box. Japanese joinery tends to look really good, even at the smaller pen box scale, IMHO.
But there are many ways to join. If you can rip thin boards, then you would have a lot of options for combining two different types of wood. And as others have mentioned, WoodTurningZ offers engraving, so you could just send the boxes in for that.