fix: add protocol override sync-check test and clarifying comment #4514

Job	Run time
Get Changes	4s
Check: source-pokeapi	2m 15s
Skipped Check: source-google-drive	6s
Check: source-hardcoded-records	2m 38s
Check: destination-motherduck	3m 15s
Check: source-shopify	6h 5m 0s
Check: source-intercom	5m 30s
	6h 18m 48s

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