If the thermostat isn't removed, yes, unless you're sure it's wide open when the antifreeze goes through, it won't circulate in the engine -- it will go straight through the bypass.
With a block properly full of antifreeze, I don't think the drain plugs are so critical. I've never removed mine.
I engineered a special winterizing cap for jugs of antifreeze by mounting a barbed plastic nipple onto one. I install that on the raw water intake, screw a full jug of antifreeze onto it, tip the jug upside down, poke a hole into the bottom of the antifreeze with a marlinspike, and run it through the engine. This gives the antifreeze a little bit of a "head" so the pump doesn't have to lift it out of a bucket.
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