(Note: This issue only affects the Live Preview and saving a custom color for Secondary Meta Text Color doesn't affect the color of the "Continue Reading" when you press Save Changes.)
When you change the Secondary Meta Text Color in the Theme Customizer, the Live Preview incorrectly modifies the link color of the "Continue Reading →" link (which appears when using the "Generate One-Sentence Excerpts" option):
$('.entry-meta a').css('color', newval);
The solution is to move the enhanced-excerpt-read-more div that contains the "Continue Reading" link outside the entry-meta div (see independent_publisher_continue_reading_link() in content.php).
This will require a bit of work to make sure the styles work properly for the Continue Reading link. This is not a priority issue since it only affects the Live Preview.
Fix issue with Customizer Live Preview and Continue Reading link. See #…
Fixed in development copy. Will go out with next release.