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Filters can go alongside, rather than underneath. If anything, there'll be less pressure in the canister, and less chance of a leak. Although it might reduce the effectiveness of any self priming functionality which relies on a siphon, which would be pretty weak without the head up to the tank.
Marine tanks don't need external filters though. It's typical to have a sump tank underneath the main tank, and equipment can all live in there, including your protein skimmer which is important.