Those hatchet marks are as old as my HOUSE !
First I'd ask: is there structural or system work that needs doing? Is the damage to the paneling so bad that the gouged panels are in danger of falling apart?
If neither of those is the case, then hooray, it's on to aesthetic (i.e. fun) decisions. At this point, old-house folk know, needing to be addressed is in the eye of the beholder.
I think the hatchet marks make a terrific story. I don't recommend un-bowing the panels, either. This is a handmade house and if anything about it even approaches square, level, or smooth, that's a tribute to the skill of the craftsmen who built it. So is the fact that it is still standing strong, even with its quirks. I think worrying about perfection takes the fun out of it.
I'd probably just gently brush a little brown onto the scraped-away areas, out of respect to the original (amazing is right!) finish. There are people on this forum who can tell you how to match the color, though I'm not one of them.
Thanks for sharing this fabulous find!