Likewise, you could just set your pool payout threshold higher, and then you will have less inputs.
True. But some people aren't comfortable with leaving rewards on a pool for extended periods of time. Presumably you trust the pool or you would not be mining there. But there's always the possibility of a hack.
Also some pools don't let you set a threshold. For example, I think that NiceHash/WestHash pays out four times a day if you've mined over a certain constant threshold. I don't think the payout threashold is configurable on that pool currently.