Great question. The journalist named in the article (Matt Broomfield) is asking authorities to delist the PKK (which clearly IS a terrorist organization targeting civilians) as a terrorist organization.
> * December 2016 Istanbul car bombing / suicide bombing near a football stadium, killing 44 people
TAK != PKK, TAK claimed responsibility. 39 of those killed were police officers. Turkish military also kills civilians while targeting opposing militia groups.
> * June 2014 Istanbul bombing / killing 6 civilians
Not intentional targeting civilians, accidental premature explosion of bomb. Only one of the attacks you've mentioned that was by the actual PKK and actually killed civilians. (e: actually no civilians killed)
To his defence, the TAK is often claimed to be a militant wing of the PKK, that handles affairs that might damage the reputation of the main organization. Like how the Provisional IRA formed fake splinter groups to pin sectarian counterattacks on.
Source on PKK targeting non-paramilitary/police/military civilians in the last 20 years?
e: I can find this from 1987 (a time when the Turkish state was also actively involved in massacring civilians) https://en.wikipedia.org/wiki/P%C4%B1narc%C4%B1k_massacre