The boulder that usually needs to be exploded with a bomb flower near the DRC entrance can not be destroyed with anything else than a bomb flower. This means gatting the bombs early doesn't skip the bottle straight away. Being able to skip the bottle allows for more routing options, as obtaining a bottle either requires going to the Bomb Isle submarine early, or requires watching the Delivery Bag cutscene and doing the quest in DRI to obtain Medli's bottle.
There are 2 ways to skip the bottle.
If you got the Deku Leaf early, then you can simply glide accross the fountain and skip the bottle. This is the fastest way to skip the bottle.
This method requires early bombs.
After getting the Delivery Bag, head on outside using the loading zone where you would usually talk to Medli and enter DRC from. If you've skipped the Delivery Bag cutscene, just head over to the room where Medli is and enter the room behind that one. Rather than going down and getting the bottle from her and proceeding through the usual method, instead we're going to align ourselves with the DRC entrance, and start a hover with our early bombs. The hover is, however, very forgiving as the wall on the left will automatically push you in the right direction. Once you're far enough into the entrance, drop and you should walk into DRC and die immediately upon entering. Don't worry; you'll still be inside once you continue. This skips the bottle with early bombs.
Do note that if you chose to skip Bottle, you will not be able to do any tricks that require Forest Water Storage or Grandma's Soup. However, Dry Storage can do most of what Forest Water storage can, so it usually works out.