I crawled up there again today. It's definitely wood - I could saw it, cut it, drill it, etc. Even after that I wanted to make sure, so I just pinched it with my pliers and it splintered wood grain. It's a 2x4 on its side. Modern milled size, so 1980s. It is not a part of the structure of the house - the chimney is on the outside of the house so it is only a part of the chimney.If it is wood and is at the connection from the old to newer section of chimney, maybe it was blocking used by the masons and accidentally left in the chimney. In which case you should be able to get it out.
I think that you're right that it is was put there by the masons as part of the chimney blocking. It is right at the point where they extended the chimney, and it looks like they flattened the top of the old chimney, laid that 2x4 on it, and started laying cinder block at that point. From there on up the chimney is cinder block and clay liner.
I'm not at all an expert, but when I got my head up there I didn't like the look of anything. the concrete work looked sloppy. A brick was missing on the interior side of the chimney, and I could see a small part of the back of my upstairs drywall! When I looked up into the cinder block portion of the chimney it just struck me as altogether sloppy.
What now? I think I can assume that the 2x4 was blocking for the masons as they extended the chimney. It's on the house side of the chimney, but not connected to the house. Should I just knock it out and hope nothing falls on me ? Then I need a liner from top to bottom?