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I believe Motorcraft sells a deep pan trans filter aside from the regular filter. Somebody will confirm but you can search around, I have seen the deep pan internal filter.
All the 4R100's have the extended pickup on the filter. The E4OD used a filter (w/o) the pickup tube for the 2wd version pan and the extended on the 4wd deeper pan. All the 4R100's basicly have the 4wd E4OD filter and pan.
Since you are adding depth to the pan and not lowering the level of the fluid in the case, it won't matter if the pickup is lower into the fluid. You are just adding volume.