This question is in no way a challenge to Rabbinical authority. This question has more to do with the philosophy of sin and how Hashem holds us accountable for our actions.
If you commit an act which was not prohibited outright in the Torah but is an act which the Rabbis extended to protect us from sin, is that the same as outright sinning against Hashem?
The Rabbis extending a rule to protect us would be seen as a guard against sin, right?
So if the action is codified by the Rabbis as prohibited but it isn't considered a sin against Hashem, does Hashem hold that against you in the same way he holds a traditional sin against you? Or is the Rabbinical fence meant for the Jews to be accountable to one another?
Chicken was not historically considered equal to other forms of meat. There were debates at the time between Rabbi Akiva and Rabbi Yose Ha-Galili which argued both sides of the issue.
They later formally expanded the rule with The Shulchan Aruch to outright prohibit the practice.
I'm speaking to examples like this. (maybe not exactly like this but the point falls into this theme)