Anyone know if there is a file I can edit to save these presets so they are the defaults?
Yes there is. It is the file 'config.ini' which you should be able to find in 'My Documents/My Games/Sid M's Civ 5'.
The second half of this file (the [game] section) contains what you are looking for. These are all pretty self explanatory. The victory conditions setting is a bunch of 1s (meaning ticked); if you wanted to make the third on the list be unticked automatically each game, you would edit this to: 11011111
; Worldsize options are WORLDSIZE_DUEL/WORLDSIZE_TINY/WORLDSIZE_SMALL/WORLDSIZE_STANDARD/WORLDSIZE_LARGE/WORLDSIZE_HUGE
WorldSize = WORLDSIZE_STANDARD
; Climate options are CLIMATE_ARID/CLIMATE_TEMPERATE/CLIMATE_TROPICAL
Climate = CLIMATE_TEMPERATE
; Sealevel options are SEALEVEL_LOW/SEALEVEL_MEDIUM/SEALEVEL_HIGH
SeaLevel = SEALEVEL_MEDIUM
; Era options are ERA_ANCIENT/ERA_CLASSICAL/ERA_MEDIEVAL/ERA_RENAISSANCE/ERA_INDUSTRIAL/ERA_MODERN
Era = ERA_ANCIENT
; GameSpeed options are GAMESPEED_QUICK/GAMESPEED_STANDARD/GAMESPEED_EPIC/GAMESPEED_MARATHON
GameSpeed = GAMESPEED_EPIC
; Victory Conditions
VictoryConditions = 11111111
; Game Options
GameOptions = EMPTY
; Max number of turns (0 for no turn limit)
MaxTurns = 0
; Allow AI in multiplayer games
EnableMultiplayerAI = 1
; GameType options are singlePlayer/spLoad
GameType = singlePlayer
; Map Script file name
Map = Assets/Maps/Continents.lua