I have experienced the clunk-clunk-clunk, with jerks, like hitting a curb twice when shifting from drive to reverse. I think the problem was that I was in too big a hurry, and shifted to reverse while it was still rolling forward a little. The first time it did it, i quickly shifted back to drive and it clunked and shuddered again in drive. The next time I stepped on the brake hard and it was ok after that. I'll just try to be more careful and deliberate in the future.
You would think that the programming of the shift mechanism and clutch would not let it shift until it was safe for the transmission, and would not let the clutch engage until the transmission was fully engaged. I believe part of the problem might be a lack of processing power in the ECU.