I'd think the Ford dealer would definately argue any warranty work. It's a gamble that you may or may not get the warranty work done in a "timely" manner, at least.
I'm not sure why you want an additional filter, unless you are expecting very severe engine usage, which would itself be an issue with the dealer for any warranty repair.
However, if you see a real need for an additional filter, I would think "feed" as the OP was concerned over. That itself, another potential voided warranty issue. If the external filter isn't receiving a fast enough flow into it so it can deliver it back to the engine, or if the filter "dries out" before it gets it's oil supply, Ford will likely say "modification that voids existing warranty". In essence, they aren't liable for an owner modifying an engine that departs from the factory issue.
I just don't think the possible benefit of another filter [especially the time and work needed to line it into the oil flow correctly] is really worth the risk of a voided warranty. Just my :2cents: .
However, there is one way around all that, have the dealer do it, then, most likely, it stays cool re warranty.