This is why string instrument players sometimes prefer to play a note not on the empty string (let's say play a A on the A-string on a cello), but instead on a lower string (e.g. first finger, fourth position on the lower D string) to accord for these imperfections. As a string instrumemt player, you pretty much only have to worry about these notes on empty strings, every other note you can "wiggle into place".
Indeed, and another factor is that a fingered note has a different tone quality.
Disclosure: String player.
And the thicker strings sound a bit different as well.
And the fingering for a given melody may just lay across the strings better one way than another.