I had thought about plugging the hole but thought it wouldn't look good.
"Look good' is very subjective - what looks good to you might look terrible to me, and vice versa. But there are things you can do to adjust that perception.
If the tube has already been glued in, you are pretty much limited to materials that you can stuff into the hole as semi-liquid or paste and that will conform to the tube. Epoxy is one option, and you can dyes, coffee or spices, or sawdust to adjust the color. It won't match the surrounding, so the objective must be to create something that is pleasingly compatible.
Some people use CA mixed with some kind of filler/colorant. Frankly, I've never had much success with CA as a filler.
Putty is another option - so-called 'tootsie roll putty' takes its name from the fact that the two components are packaged in a concentric roll, and you just cut off as much as you need and knead to blend. Milliput is a similar product tin which the two components are packaged side-by-side. Putty has an advantage over two-component epoxy that you generally won't get air bubbles that won't appear until you turn down the blank.
If you have not yet drilled and inserted the tube, you could use either a dowel or a plug - the difference between them is the direction of the grain. A dowel that passes through the center of the blank will likely leave end grain on the side of the finished turning that will never match the surrounding side grain. With a plug, you might be able to get an approximate side grain or color match. Getting a dowel or plug that matches the surround wood could be a challenge unless the blank is longer than you need for the pen, and you can salvage enough from the end to make your infill.
But in either case, if the hole is discolored because the original seat mounting bolt was corroded, you either have to accept that as an artifact of the original purpose of the wood (in which case, attempting to get a close match with the surrounding material won't make a lot of sense), or else drill out the hole to remove that discoloration which then requires a larger dowel or plug. Trying to get a grain and color match would be a lot of work, and you would have to ask yourself if you want to put that much effort into a pen.
So if you conclude that it doesn't make sense try to make the hole invisible, then it might be better to emphasize and make it look interesting. In that case, a dowel or plug from contrasting wood might be ideal.
As has been said many times in this forum - there are many ways to skin the cat. The objective is to have fun applying whatever solution you choose to use.
cheers.
