Yeah, it's because it's writing data, so I think it sort of pauses whatever is happening, though that's probably not what it's actually doing. I do know that it's pretty much writing / encoding all the available data (entire game) into a save file. Usually only takes a second or so.
I still don't understand why you want it to overwrite the data, if you are talking about the autosave file slot you are using for new game, then you only need to write it the first ever time someone launches a new game.
Quick note: technically while you are in the development phase, you really shouldn't be using save files anyway as they become invalid whenever you make any significant changes to your project. Why? Because it's likely that old save files that were created before any changes contain incorrect or missing data due to them containing data written to them from a prior version.