Generally, it's so that the national polity can invest in specific regional polities without fear that they'll take the money and run, or abscond with strategic assets critical to the development of other regions.

It's basically a checklist item for a negotiated diplomatic withdrawal, to avoid triggering a knee-jerk military suppression of the unlawful rebellion. If "the rest of the country" does not agree, and won't negotiate, secession is still possible, it just means winning the civil war.