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I'm not going to say you're wrong, and your experience shows the something has changed or been damaged.
There are no oilers in Honda manual transmissions. There's no pump, nothing runs off the input shaft. It's just a box of gears sitting in an oil bath. They're dead simple.
What might have happened is, the synchros might be getting worn. The larger the RPM difference when shifting, the more work the synchros need to do. An engine not spinning creates a larger difference between input and output shaft, but in practice it's the same as if you revved the engine 6-800rpm higher before shifting. You're also likely shifting more frequently.
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