You have to look at the drive train as three components separated at two points...
something like this:
You can control the speed of the engine (at least I hope so)
You can control the speed of the output shaft (by varying road speed)
When you mis-shift into neutral with the clutch in you have disconnected the gearbox shaft from both the output shaft and engine and no longer have control over it's speed.
The clunk your hearing when you shift into gear with the clutch in is the gearbox shaft matching the speed of the output shaft, matching RPM perfectly will do no good in this instance. You will still get a clunk.
To avoid the clunk you have to leave it in neutral, let the clutch out (slowly) to get the gearbox shaft to the correct speed then once rpm is matched to road speed pull the clutch in and quickly shift into gear, then let the clutch back out.
Either that or clutch in and in neutral until your stationary and start again...
The reason bliping the throttle helps is that there is still a small amount of force transmitted through the clutch even though you have it pulled in (similar principle of operation to an auto gearbox's torque converter), the engine will be going considerably faster than the gearbox shaft but the gearbox shaft will nevertheless speed up a little, causing its speed to approach the speed of the output shaft resulting in a smaller clunk.
Does that clear it up a little?