Whatever goes into the reservoir goes into the whole loop. Assuming that the overflow system is properly sealed and that pressures are equalized accordingly, coolant that flows through the pipe. You're just wasting your coolant by making it sit in a place where it doesn't do anything.
If your loop has rust, it simply means that its corrosion inhibitors have expired.
That rust actually comes from the engine, mostly comes from your cylinder lining. It is accelerated by water.
Cavitation is not a pleasant thing.





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