Sure. It was explained by someone else, but I can not find the post atm. Anyway: the charge time is counted after you throw a boom. Thus, all it can do is help charge a flash kick even before the boom is released or make sure after a given boom you start charging as soon as possible. However, if you want to keep throwing booms as fast as you could, any frame you spend in backwards direction without charging, that is, just before you throw a boom, is a waste as it adds to the virtual start-up of the move. To better illustrate it, let us assume the charge time for a boom is just 4 frames, and the recovery is whatever less than that. Thus, the perfect series of commands for spamming booms would be
back - back - back - back - towards + punch - back - back - back - back - towards + punch - ...
which can be resumed as
(back - back - back - back - towards + punch) repeat
which means one boom each 5 frames. Now let us assume the human player is slower and his execution is such that actually demands a frame with the stick on neutral position when switching between backwards and towards. Thus, the series of commands, with the usual method, would be
back - back - back - back - neutral - towards + punch - neutral - back - back - back - back - neutral + towards + punch - ...
which can be summarized as
(back - back - back - back - neutral - towards + punch - neutral) repeat
which is one boom each 7 frames. It is worse, but hey, we ain’t machines.
Now, let us try to modify the usual method as in the pre-charge method, with the same execution limitation, to see what happens. For this, we will keep the same joystick pattern, but press punch as soon as we reach back. We assume we have this consistency to be able to press punch the very same frame we move the stick to the backwards direction, every time. We obtain
back + punch - back - back - back - neutral - towards - neutral - back + punch - back - back - back - neutral + towards - ...
which can be summarized as
(back - back - back - neutral - towards - neutral - back + punch) repeat
This might have given one boom each 7 frames, but there is a problem: the charge time for the same special only counts after you use it, which is when you press punch for the sonic boom. And in this situation one only has effectively charged for 3 frames after he or she presses punch, being that it was assumed that the move demands a charge of 4. Thus, one extra frame is needed for the pre-charge method, thus making it strictly worse when it comes to throwing many booms in quick succession. To make it as fast as possible, no pre-charge should be used, with punch being presses either in towards or neutral directions.
Edit: the merit of the content is for the one who has tested it. Errors or bad grammar is my fault.