I've managed to figure out #1 and #3 but I still can't get #2.
Using a druid as an example: in a raid I want to be able to see only the HoTs I have cast on the raid unit frames - I can do that by selecting Default Buffs, Mine. But I'd also like to be able to see at a glance whether everyone has Gift of the Wild & Thorns regardless of whether I cast it or not. I cannot figure out how to have both of these functions at the same time!
You most certainly can do this. The only thing you can't do is show an icon for a debuff that is missing.
To do what you want is pretty easy. Since everyone seems convinced that you can't let's walk through how to do it.
a) /pitbull, Modules, Aura, Aura filter editor.
b) Go to the Advanced tab and select Druid friend buffs.
c) In the New filter box type "Extra Buffs". You'll now have a filter that's identical to the built in Druid friend buffs filter but is named Extra buffs. This filter is going to be Extra buffs that we want to always be able to see. Uncheck everything but Gift of the Wild, Thorns and Mark of the Wild.
d) Now scroll to the top and choose Default buffs mine.
e) In the New filter box type Mine+Buffs (or whatever you want to call it).
f) Set all the Filter dropdowns to None until you only have one. Technically you could just add what we're going to do to the end, but doing it in the manner I'll show you will make your filter dependent upon the built in one so if it changes you don't have to do anything to gain the changes.
g) Now for the first Filter drop down choose Default buffs, mine. In the second choose Extra Buffs. In the first opreator field change it to OR. Everything else can be left alone.
h) Now go under the Layout editor to the layout you want to use this on, go to Auras, Filters, Buffs and choose the Mine+Buffs filter.
Useful things to know about meta filters. AND bind more closely than OR. So if you have something that looks like this:
foo and bar or baz
foo and bar must be true or baz must be true.
If you want to force ORs to bind more closely than an AND just put them in a separate meta filter. Each filter is evaluated separately so that can get you want you want in that circumstance.
There really is almost nothing you can't do with the aura filtering system in PB4. Some things might take a bit more hoop jumping than I'd like but the design allows for a fairly simple UI and filtering code.