Hi,
Looks to me like the wire might be a red herring... They are moving at exactly the right time, it's just the passenger one is stopping mid way probably due to a minor misalignment in the boot locking mechanism. I believe that the wire which pulls the flap down is attached to the cylindrical lock which wraps itself round the pivot which grips it (a bit like a car door mechanism).....
I think the delay is because as the lock engages, it is hitting the pivot, pulling it down further to then wrap round it to engage. Hence the delay...
It may be worth getting the dealer to look at it, or even better, send your video to VW Tech Support and get them to review it.... Let them advise if it should be looked at.... It is quite possible that it may correct itself in due course.. Please also check that the boot rubber around that area is installed correctly and not stopping the lid from closing correctly at that point. This can be looked at when the boot lid if fully open....
Also, hate to say it, but when you installed the MOD, did you make sure that the boot rubber and other trims were fitted back correctly, including the supports on the left (The plastic cap on the little arm and the rubber cap)...
If some boot rubber seal is raised in that area, it can cause similar symptoms in my opinion.