How deos this clock generator work?
Every time the capacitor charges (in one direction or the other), the comparator eventually flips its output to start the reverse charging process. The moment it flips, the D type changes state and latches. This initiates the reverse charging process and the comparator immediately flips back. But, importantly, the D type remains latched to allow the reverse charging part of the cycle to reach completion.
So, the D type has to latch or it won't continue the reverse charging process to proper completion. The comparator only changes its output state for a very brief period of time hence the D type MUST latch until the reverse charging process completes.
The D type in effect divides the comparator output by two but so what - this is needed to make the circuit work.