Well... the process of that seedling growing into the big tree over 40 years is what takes carbon out of the atmosphere. The carbon just goes into the tree's biomass. So - long term, if you have a steady state where the biomass of the trees you're talking about remains roughly constant (or dips but comes back to the same level) - it is carbon neutral. Even if you're cutting down big trees and planting seedlings.

Of course, you're right, there's nuance there. If you start with a mature forest, cut it all down, and replant it with seedlings, that's not a steady state (yet) - particularly when you take ecosystem effects into account, I suspect.