This is simply a technicality in order to ensure an official game. The clock does stop as soon as the ball clears the bottom of the net. It is generally accepted that a player cannot release his shot in under .4 seconds but in order to consummate a complete official game the clock must end up at 0:00. The same goes for football games that end on kneel downs. If there's little enough time the defense won't get the ball again, but if the clock doesn't read 0:00 it's not a complete game so the offense chooses to kneel the ball until the clock runs out.
A full normal shot is not possible (watch this - https://www.youtube.com/watch?v=HOiH1eVCggw) in less than .4 seconds. Notice how the narrator says that Curry's shot is the quickest they have ever analyzed. Also about shooting in under .3 seconds here's the rule - http://www.nba.com/analysis/rules_l.html?nav=ArticleList .
Definition of basket -
RULE NO. 5—SCORING AND TIMING
a. A legal field goal or free throw attempt shall b
e scored when a ball from the playing
area enters the basket from above and remains in or
passes through the net.
Section V—Stoppage of Timing Devices
a. The timing devices shall be stopped whenever the
official’s whistle sounds.
b. The timing devices shall be stopped:
(1) During the last minute of the first, second and
third periods following a success-
ful field goal attempt.
(2) During the last two minutes of regulation play a
nd/or overtime(s) following a
successful field goal attempt.
This means that the ball must clear the bottom of the net to be considered a legal field goal at which point the clock is to be stopped.