What happens if you hold your hand directly above a flame? The heat goes up and burns the hand. What happens if a chimney is blocked? The smoke is not able to flow up through it, and the smoke is all trapped down in the house.
The energy naturally wants to flow upward through your body. But all of your chakras must be open and flowing nicely. So the energy can flow through you without becoming blocked.
If you put energy into a lower chakra when any of the chakras above it is closed, there is nowhere for the energy to flow to because it is blocked. And it will quickly build up a lot of pressure and heat inside of your body right under the closed chakra. This is a very painful experience, and it is not healthy for you.
If you start from the top, the first thing you are doing is removing blockages so everything is able to flow nicely. So you will never be in that painful situation. It is building the chimney before starting the fire, which is the safest and most comfortable way of working.
This is most important when first opening the chakras. The first few times you are working on them, until you are able to feel them flowing energy. After they are opened, you can safely work from any direction you want and you can safely start from the bottom because the chimney is already there.