What does the expression mean?

A first observation, then, is that as the number of holdings increases, covariance becomes increasingly important, all else equal.

all else equal = if all other things that could affect the situation in question remain the same

Example:
All else equal, we will go on a picnic tomorrow.

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If the weather remains sunny, if the car remains in good condition, if all the participants remain available etc., we will go on a picnic tomorrow.

Other commonly used variations on this phrase are “everything else being equal”, or “all other things being equal”.