Snowball Bowling is definitely the highest return method for earning. For each strike, you get a return of 280 rupees (cost of 20, reward of 300, leads to a net of +280). The Chest game is only 200 gain per success. In addition, Snowball bowling is primarily skill based, whereas the chest game is RNG. As far as the cold gear goes, if you're doing All Dungeons, you'll be going to the Rito village regardless, and you can buy the cold gear there (you'll need to for the dungeon anyway). The 2 cheapest pieces are the chest and leggings, totaling 1150 rupees to buy. Or, if you got the Warm Doublet in the beginning, you can combine that with one piece and be set.

There's a trade-off in skipping runes at the beginning. Yes it may save time at the beginning, but will it save time later in the run? You basically NEED Magnesis for multiple sections of the game (several fights I've gotten to require it). You'll also NEED Magnesis to get multiple Korok Seeds. Cryonis is required to complete multiple Shrine challenges as well. Trying to find alternate ways to do them would possibly take longer than skipping the rune in the first place.

As far as 100% goes, it would be a heck of a run. My thoughts are that it would be:

• All Shrines
• All Divine Beasts
• All Korok Seeds
• All Memories
• All Quests (if that's even possible, might be difficult to quantify since it'll likely be quite some time before all quests are discovered), could be limited to all main quests
• All Towers
• All Fairy Fountains
• All Rune Upgrades
• Complete Hyrule Compendium on the Sheikah Slate (might take longer than All Quests would...)

Enemies in the overworld all respawn with the Blood Moons, so "All Field Bosses (Hinox/Lynel/others)" would be impossible, as they reset with the Blood Moon. Alternatively, it could be limited to just the items present on the loading screens (Spirit Orbs, Korok Seeds, Divine Beasts, Shrine Count), for ease of checking completion, and to make the run practical, even if it wouldn't be a "true" 100%. On the other hand, if the game gives a % Completion score upon beating Calamity Ganon, that could be used for the definition (whatever it takes to get that to 100%).