It's particularly slow on my machine then. I measured ~5 seconds mostly due to the time it takes to save the file/unflatten/flatten. I am not on a low end PC either.
Here are my specs:
Windows 10 64 bit
3.25 GHz (Overclocked to 3.75 GHz) AMD Ryzen 3 2200G
4.0 GB of RAM (I know it's not that much haha)
Two identical SPCC SSDs (I get good write/read speeds usually and saving a small image file wouldn't take that long).
An NVIDIA GeForce GT 730 (This card isn't that terrible. I am able to get FPS in the 80s and 90s in a lot of modern 3D games, for example Minecraft. I don't have performance problems with most software/games.)
Paint.net version 4.2.6.
Additionally you are saving to a non layered file if you are using Ctrl+S otherwise it would overwrite my layered pdn file. Here is what I do:
Ctrl+S
Ctrl+Shift+S
Select png, press enter, press enter to override
Press enter to accept save options
Press enter to flatten
Press ctrl+z to unflatten.
For one thing, I shouldn't have to write a macro to save files. Secondly, I wouldn't be making a post if this wasn't effecting me my workflow. Trust me when I say that I sometimes spend more time waiting for PDN to save than actually working.