Intersample variability is a type of confound.

No it isn't

Or maybe you have a weird definition of confounding?

I use the standard definition of confounding based on whether E(Y| X=x) = E(Y| Do(X=x)), and think about it in terms of whether there exists a backdoor path between X and Y.

Either way, confounding is a separate problem from causation.

The concept of confounding is defined relative to the causal query of interest. If you don't believe me, try to come up with a coherent definition of confounding that does not depend on the causal question.

You can isolate the confounding variables from the independent variable to determine the correlation between x and y without determining a causal relationship.

With standard statistical techniques you will be able to determine the correlation between X and Y. You will also be able to determine the correlation between X and Y conditional on Z. These are both valid questions and they are both are true correlations. Whether either of those correlations is interesting depends on your causal question and on whether Z is a confounder for that particular query.

You can also determine the presence of a causal relationship without isolating the independent variable from possible confounding variables.

No you can't. (Unless you have an instrumental variable, in which case you have to make the assumption that the instrument is unconfounded instead of the treatment of interest)