You are correct in claiming that the Confederate constitution is nearly word for word a copy of the US Constitution. However, I disagree with you that the few changes that exist expanded state power/restricted central power.
Below are some limitations to state power that are NOT slave related:
No State shall enter into any treaty, alliance, or confederation; grant letters of marque and reprisal; coin money; make anything but gold and silver coin a tender in payment of debts; pass any bill of attainder, or ex post facto law, or law impairing the obligation of contracts; or grant any title of nobility.
No State shall, without the consent of the Congress, lay any imposts or duties on imports or exports, except what may be absolutely necessary for executing its inspection laws; and the net produce of all duties and imposts, laid by any State on imports, or exports, shall be for the use of the Treasury of the Confederate States; and all such laws shall be subject to the revision and control of Congress.
No State shall, without the consent of Congress, lay any duty on tonnage, except on seagoing vessels, for the improvement of its rivers and harbors navigated by the said vessels; but such duties shall not conflict with any treaties of the Confederate States with foreign nations; and any surplus revenue thus derived shall, after making such improvement, be paid into the common treasury. Nor shall any State keep troops or ships of war in time of peace, enter into any agreement or compact with another State, or with a foreign power, or engage in war, unless actually invaded, or in such imminent danger as will not admit of delay. But when any river divides or flows through two or more States they may enter into compacts with each other to improve the navigation thereof.
In addition, the congress of the CSA was given the power over state militias. For instance the CSA constitution gives their congress the right to:
provide for calling forth the militia to execute the laws of the Confederate States, suppress insurrections, and repel invasions.
provide for organizing, arming, and disciplining the militia, and for governing such part of them as may be employed in the service of the Confederate States; reserving to the States, respectively, the appointment of the officers, and the authority of training the militia according to the discipline prescribed by Congress.
The excerpt you list "nor shall any duties or taxes on importations from foreign nations be laid to promote or foster any branch of industry; and all duties, imposts, and excises shall be uniform throughout the Confederate States" is a restriction on central power. What that is saying, is that the central government can't cherry pick an industry to promote or harm. It is restriction on central power, but not an extension of state power. In fact, I know of nothing in the CSA constitution that gives states more leeway in governing their own business.
You mention that the Confederate Constitution contains "dozens of limitations on federal powers in regards to the states". I am only aware of one (the one you listed). I am aware of a half dozen ways that the Confederate Constitution restricts states more. If you want to make you case, then point out these novel central government restrictions or state government expansions.