I understand that those colonies were established not where pre-existing settlements were but essentially near them. The same is claimed for Alexandria in Egypt. A few people probably already lived where the colonies were established but not within a significant settlement, at least compared with the new colony or city. That was possibly a difference for Sinope if Herodotus had it right. Obviously whether on a previous settlement or not Sinope was or became Greek given it went on to lead to further Greek colonies in the region.

unlike the British colonies which always had a local identity

I picked Madras and Calcutta as examples because they were established where only villages existed. There was a tribe settled in Manhattan, but NYC's considered to be established by the Dutch even though it became English and then American. In many other cities, there was a local identity which wasn't particularly affected by the colonialists.

Also, I would argue that even hellenised does not mean that something isn't/wasn't Greek, just like Turkified does not mean it isn't/wasn't Turkish.

Certainly. These Greek colonies I've named became French, Italian and Turkish over time. People and/or identities come and go, leaving their marks.