What do you mean by the "lower door"? Are you thinking to only put PPF on the top half of your doors?! That is going to look extremely awkward in a month or two of winter when that seam line gets highlighted by dirt and grime. You'll have a dirt pinstripe running across your entire door...!
Not only that but I think the lower half of your doors (the bits closest to the road and directly behind your front tires) are the most vulnerable so I don't see how excluding the lower half would make any logical sense. If anything, that's the one part you SHOULD cover in PPF.
My suggestion for anyone thinking about PPF is to always do complete panels... the marginal cost of a full panel vs a partial panel is probably quite minimal but the benefits are huge if you care anything about aesthetics (which, if you're asking the question, you probably do since PPF is literally trying to preserve the aesthetic). The seams are where dirt will accumulate and those lines will show up very distinctly after a month or two of snowy weather and will be difficult/near impossible to fully clean. Further, that dirt will cause a bit of lifting and pealing in the film. If you're trying to save money, partial panels are NOT the way to go. Instead, I would focus on specific panels. IMO, the order of importance are the rear doors and the front bumper, then the hood, then the front doors, then finally the trunk hatch and rear bumper.
Also, depending on your intention with the PPF, the trunk hatch actually does help in that this section gets very dirty quickly. While this section does not get abused like the rear doors, I find that if I drive in the rain, I'll always get water spots back there but nowhere else (I have ceramic coating). While the PPF itself does not necessarily wick away water the same way as ceramic, it does wick better than bare paint and will add some protection against stains/paint degradation over time. Probably a minimal benefit but you can decide if it's worth it.
