Productivity systems and perverse incentives
Productivity software makes your life more legible and more structured. That's good, but it's not all good. Whether or not some particular tool is good, bad, efficient, inefficient, or anything else, there are some drawbacks that are common to most or all productivity systems.
First, because they make organizing tasks and projects feel good, they can incentivize you to take on too many tasks. The process of judiciously rejecting things is rarely modeled or rewarded in the software. I'm sure that some tools, somewhere, do this, but the standard workflow is to get set up and then put as much into the system as possible. Or, at least, that's what I tend to do.
Second, they tend to add friction to the process of actually completing things. Good tools minimize this, but it is rarely zero. There's a burden just in the knowledge that, by doing something, you'll have to update an in-software model of your life. This sort of friction is damaging, especially to the project of avoiding zero outputs.
Again, the benefits in legibility and structure from productivity software often far outweighs these. But it's worth knowing the dangers that come less with specific tools and more with the whole project of using productivity tools.