What I noticed on my 2.5T, with the level at the F mark, after engine reaching operating temp, the fluid will rise about 3/8" to 1/2" or so above the F line.
How did the air get in? I think that's simple. If/when the reservoir runs low (why is the kia system atmosphere venting to begin with!?@#), there's no more fluid to suck in as the coolant cools and contracts. Instead air is sucked in. Now air is free to circulate about within the cooling system.
tl;dr, IMO it's important to keep the res levels above L.
This is the first car i've had where I had to top off coolant in between fluid drain/fills. In the coolant smell thread, I linked to a thread on the k5 forum where an owner heard coolant gurgling sounds while driving. Turns out his res was exceptionally low.
As for correcting this, I suppose one can try one of those lisle burp funnels. They attach to the radiator at the cap fitting. You fill up the funnel ~half way. Allow the engine to warm up and fans to cycle at least twice while adding fluid to keep the funnel full.
I'd have to try this if I had the OP's issue. My method when doing a drain/fill is to use a vacuum filler (
https://www.amazon.com/UView-550000-Airlift-Cooling-Checker/dp/B0002SRH5G). There's no need to burp anything or have thermostat cycle.
The OP indicated engine was replaced 4K ago. Possible they didn't bleed it properly thoroughly. IMO, it's up to the owner to keep track of fluids, esp on a new engine. Assume the mechanic putting it together is incompetent.
For you GT2 owners, does the dash indicate what the actual coolant temp is?