Personally, I recommend to save for the higher runes in "Eight Inner Gates" feature. The reasoning is because the runes cannot upgrade from purple to gold runes. You c@n use subsequent materials to increase the level of the specific rarity/tier of the rune, but not to upgrade the rarity/tier itself. This means, it is more beneficial in the long run to save and get the highest tier rune you can in the "Exchange Chakra" shop. There are many other reasoning of course (as much as the mind can imagine =p), such as the reasoning could depend on your build. Many of the builds currently focus a lot of power and stats towards the Position 1 advantage. So saving to get the better Quick Rune c*so become advantageous in that respect.

TLDR: In my opinion, saving for the Yellow Quick Rune is the better choice.