No, the pressure upon the top seal will be 1000lbs, while the pressure upon the bottom seal will be greater. How much so depends upon the size of the canister.
For example if the bottom seal is physically 1m lower than the top seal, the pressure upon it is roughly 1001lb.
If the canister is the size of a matchbox, then the difference would be minimal.
If the canister was a sub, sticking out of the bottom of the seabed, the differences could be 10-20 lbs per seal.
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