No, what is called the Charter of Fundamental Rights is
part of the Lisbon Treaty (which itself is just a series of amendments to the previous treaties on the European Union). It is, btw, what the European Court of Justice is intended to enforce.
You can see this from the (lengthy) title:
"Consolidated versions of the Treaty on European Union and the Treaty on the Functioning of the European Union - Consolidated version of the Treaty on European Union - Protocols - Declarations annexed to the Final Act of the Intergovernmental Conference which adopted the Treaty of Lisbon, signed on 13 December 2007 "
Now you are right that what prompted these carveouts was fear that the EU would promulgate various human rights provisions and force them on Poland, specifically abortion/gay marriage and other measures inconsistent with Polish Catholicism.
This is part of the strategic ambiguity of the Lisbon treaty, with conflicting claims in the treaty meant to satisfy different parties. Thus in one section it states that national laws will be respected, and in another it has a supremacy clause, and in a third it says the area of competence is subordinate to national parliaments.
All meant to create strategic ambiguity to get the thing signed.
But even more importantly for Poland as well as other countries, national Supreme Courts must enforce the constitution of each nation and that constitution is the Supreme Law of the land. A treaty cannot abbrogate a constitution. Thus Polish judges cannot side with a treaty when it conflicts with the Polish constitution. Recognition of this is respecting the rule of law, not violating it.
And when there is a conflict between a law and a treaty, the judges need to side with the law rather than the treaty. The treaty is an outward promise to the rest of the EU and the EU can find that Poland violated its treaty obligations, which would be a matter for the Polish Ambassadors and representatives to deal with, but unless the Polish constitution is amended to recognize the acts of the EU parliament as having the force of law in Poland, then the judges have to enforce the Polish law as enacted by the legitimate law creating mechanisms spelled out in the constitution.
Ironically, this insistence on enforcing the law and the constitution is what the EU calls "violating the rule of law".
And the same thing is true in the Czech republic -- when there is a conflict between an EU law and the Czech constitution, then judges have to side with the Constitution:
https://journals.muni.cz/cpvp/article/view/6637
This came up as the Czechs are seeking to enshrine the right to bear arms in the constitution, so it is very relevant to know who ends up winning: EU gun regulations or Czech regulations. Well, the Czech regulations win.
This should be obvious, if the EU requires its rulings to override national law without being enacted by the national Parliament, then it should have required Constitutional changes to delegate the creation of lawmaking to the EU before letting the nation sign the treaty.
But then no nation would join the EU.
Therefore you have this strategic ambiguity and feigned outrage whenever a supreme court says it is beholden to its national constitution rather than to a treaty (in those cases where there is a conflict).
There is a process for changing the constitution, and it is much harder than the process for signing a treaty. This is because the constitution specifies how laws are to be created and interpreted, not treaties.
Treaties are agreements between nations, but within a nation, the constitution is supreme, and that will remain the case unless the Polish constitution is changed. Polish judges are expected to enforce that constitution, and if the EU finds that Poland has not respected its treaty obligations, it can try to withhold aid or take some other EU specific measure against Poland, but it's not the job of judges to allow treaties to change constitutions.