Problem stems from the fact the keys and manifest have to be with the container if it's locked to allow customs searches, or the container has to be left accessible. As yer not going to send an armed escort thru every Country the container passes, there's nothing you can do except pray that the 'officials' along the way are kosher and that Rangit Abdul your friendly driver is of fine mettle and not open to bribes.. or being made to open containers at gunpoint..
The only way round it would to be to air freight everything in. Not that easy a thing to achieve and there arent enough Aircraft to achieve it.
If the Container is locked, it's no problem, they'll immediately ask to see what's inside and cut the weld, padlock, etc that's securing it. Theyre within their rights to do so.
Even cunning packing wont help. shoving the heaviest items you can find in your unit by the back doors wont help, they'll just get dragged out the way and the other items listed on the manifest searched for and thru.
In short, there's no way of avoiding it. It's not the Loggies fault, they can only do what the movement guys say. It's not the Movement and RMP's fault, they just say what the rules concerning international freight movement say.