I'm on the same wave length... but with problems
The "Lowepro Omni trekker Extreme" I feel would be the answer for you in an anything other than off-road motorbike world.
It fits into a Peli 1550 and has its own rucksac, plus it also becomes a top loading sling shoulder bag. - thats a pretty impressive set of credentials.
Only snag is the level of (and type of) padding between the case and the gear is insufficient to protect against heavy judders.
to give you an idea I am thinking of the Dodoma road before the rains, or anything around Isiolo. This is where most of my experiments have come undone.
If you are on tarmac roads then this is all overkill and the lowepro peli option is sufficient provided you protect against engine vibration.
What lenses are you using? in the Pelicase 1550 a Canon 70-200 f2.8 will not alow sufficient room to not get jarred, whereas the f4 version is fine. likewise a full sized body should not be stood upright. Got to admit that most of my experiments were with nikon manual focus lenses, which were extremely robust, yet still died!
Mixed results with the Ammo cases: Everything I am doing is home made... Initially I had 4 Nato grenade ammo cases, two on each side, one on top of the other inside a "cage" which gave me good compartementalisation. But it was heavy and diddnt quite work as it was not versatile enough.(but very very waterproof and indestructible)
Now I've brought 2 "side" opening ammo boxes, which probably are not waterproof! They are 64x33x20 cm.
I have not made it yet, but basically I am mounting a ladder frame with support under the boxes onto each box. On the top of the frame will be a solid metal axle. this will fit into a U shaped iron on the bike frame to create a pivot for the case.
This alows the case to swing upwards so you can load it horizontally.
Then I am mounting a square support arm from the foot pegs around the rear of the bike up to the Exhaust/rack mounts, with two horizontally parralel main frame arms. On the top section I will have the U tube. which the top of the panniers fit into. and on the bottom section some form of lock, easy to do, not concernd
When the pannier swings down it will rest against the frame, and have another U shaped iron for the bottom parralel to provide verticle support in both directions. with the rest of the strain being taken up by the hinges.
I guess watch this space for the ammo cases. Incidently the cases cost me £19.80 including a whopping £8 for shipping! The steel so far I have got from the dump, amazing whats there, so thats been free, but I am going down to the steel merchants next week for the correct dimensions that I want... £30 including welding rods
RIGHT onto that blasted topbox.
There is a marine product called 5200, its a type of silicone sealant. I am going to be using this to attach the engine mount rubbers to the pelicase at all four extreme corners (having removed the top screw) I know it sounds daft, but I have absolute confidence in the product, (long story involving incorrect placement of a winch on a yacht...) Just remember it doesnt come off... ever. Thus there is no penetration of the pelicase for transmission of vibration sufficient to unscrew the mirror box (Nikon FE2)
A decent 1cm layer of this will provide sufficient absorption from those miniscule vibrations that rattle and unscrew lens elements (80-200 f4 Nikkor)
Then the engine mounts will be mounted onto a 5 inch long metal arm using a layer of cork and then a layer of rubber squeezed above and below the arm and washer. This arm will extend inwards to the rear rack frame. The idea here being that the arms will absorp some of the harder juddering (Tamron 60-300)
This will be my last effort at building a top box that I will be happy with. if I am still not happy, I am just going to build a pinhole camera!
I think I have used up too much time, good luck with your ideas, and give me a shout if you come up with a winner (Dont tell me if it all goes wrong.. so many cameras its depressing)