At first glance the first two paragraphs are hand wavy enough that it is pretty clear that you exaggerated when you said "simply ntp synch requests" and things get a lot worse after paying any attention to the details in your post.

Timezones and NTP? NTP does not use time zones so I am not sure what that has to do with anything.

Exit nodes forging ntp responses? That is going to be pretty tough. Last time I checked tor has a tcp fetish and ntp is squarely in the udp camp.

I checked the reddit link. Lets skip over the fact that you said "identify a client" and the reddit link is about hidden services. In order to work it requires that the hidden service serves http, serves http over plain ipv4, and is running on a computer that is also a relay. So that is not "simple" but most importantly it has very little to do with ntp requests.

I'm not going to lie, I stopped reading the whonix documentation after the first three paragraphs and i have pasted them below:

  Don't wonder... To prevent against time zone leaks, the system clock
  inside Whonix was set to UTC. This means it may be a few hours before
  or ahead of your host system clock. Do not change!

  On the host. If you were a user of TorBOX 0.2.1 or below and removed
  NTP, restore it now.

    sudo apt-get install ntpd

Can you see why I stopped reading when I did? It seems like you may have disremembered the details of the "simple ntp synch requests" can give a way a users identity attack.