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.
Magiobiwan, I think this concept primarily applies to Any%, where magnesis isn't necessary
You need magnesis for Thunderblight, not stasis. But regardless, you need to grab the rune to pass the shrine.
This isn't really related to skipping the actual rune but you do not need to use a bomb to get over there. You can do a shield surf onto the boulder and over:
(Timestamps don't seem to work on the embed so skip to 21s or so to see it)