The Gemara (and also later poskim) give many examples that kinyan kesef still holds because the reason for the gezera does not hold. Similarly the gemara gives examples when onaah does not apply because the other side was aware of the situation.
In many cases in Shas the gemara applies "lo plug" even when the reasons of a gezerah don't apply. Why don't we apply "lo plug" to kinyan kesef and onaah even when the reasons for the gezerah don't apply.
Ona'ah is not a Gezairah, it is a Din D'Oraisa and the Rabanan were merely describing which cases are included in the Din.
With regard to Kinyan Kesef, although we do see many times that "Lo Plug" applies in cases of Takanos, we also find many cases of "Milsa d'lo Shechicha Lo Gazru Rabanan" and other restrictions on Gezeiros when the reasoning did not apply. We see that "Lo Plug" is not a steadfast rule, but rather a tool the Chachamim used to srengthen the Gezeirah in similar situations where they felt that without a general rule the Gezeirah would not hold.