You got it with your edit.
Of course the virtual machine assumes they are atomic as you first stated, but the reality of the sharding is they can't be.
Building the virtual machine was the fun, easy part. The consensus scaling was the hard part which they should have done first even before raising ICO money. That is disgraceful.
The only way around this that I can see is to make Ether non fungible, which is a bit of a problem for a currency.
Even that wouldn't work because as you pointed out, the entity running the script pays the gas, and that entity can not in every case have its gas balance in the partition that validates the script.
But gas never was going to work economically any way, because all the validators need to be compensated, not just the one who wins the block. Any means of equal sharing the gas between all validators will be Sybil attacked (again any arguments about changing this reality via consensus-by-betting would return to the fact that proof-of-stake or deposits are self-referential and all that entails). And any non-equal sharing means the consensus becomes centralized over time according to the rule that
the one with the most resources has the most economies-of-scale.