Editing 4k Feature Doc, Need some help

To answer your questions:

1.) Proxys are only necessary if you system cannot handle the files sizes of your footage. If you want to work online in PP I would recommend decode everything into the same codec. ProRes will work just fine because it's made for NLE software. Depending on the bitrates different versions of ProRes can be used. For the 5D and the A7s II I would use ProRes 422 LT and for the F5 footage I'd use ProRes 422 HQ (except it's 444 color coded footage then use ProRes 4444).
It's also depending on what resolution you want the film to be. If you have the project in 1080 it will work much smother than in 4K in smaller machines.
But especially decoding the footage into other codecs will make it easier.

2.) This setup seems to right to handle the footage. Just keep all app data on the SSD and have the rest of the harddrive space free.
Otherwise, if you have 3K $ Budget for a editing system I would recommend a 5K iMac and a 2nd monitor plus some RAM memory the install later on (it's cheaper then buy the RAM directly build-in from Apple).
This setup will give you a really nice display able to screen your footage natively and with very true color and it's also made for 4K video edit. But it has less hardware power than the configuration you got for your MacBook. I would say this depends on what you need. For longterm edit I think it's better having a nice big screen which makes it easy to overlook everything than a small 15" monitor. Also it depends if you want to edit & travel with your computer or not.
But from my own experience (hardwere wise) I can tell you that a 5K iMac just works fine handling that kind of files and footage.

3.) If you decode your footage you need to store your new files temporarely. If you have 12 TB of footage now count about 14-16 TB of footage in ProRes (yes, this is the downside of decoding). If you decode it stepp for stepp you will need 20 TB in total for your project. So I would say another 4 TB would do the job (considering that you will delete the old files from that same drive but keeping a backup of them on some other drive).

I hope, I could help you with your questions and good luck for edit!

I have a lot less powerful system and she edit mostly xdcam HD files with premiere. If i have to cut avchd files or h264 the playback and editing is really slow. But i would suggest you test this with your system if it works smooth with your files stick with it i would say. If you likte to collor grade in resolve or so you can still export your timeline in profess hq. The system you mention will definitely cut 4k. The problem sometimes with long gop files is that it asks a lot of math to code and decode the material so it makes it hard on your system. You can also transcode al of your material in proress proxy files edit it and relink with your original footage, create a consolidate transcode tis footage to profess hq for colour grading.

I wouldn't waste my time or storage space transcoding, this is not usually possible for documentaries because of the amount of footage.

I have edited three feature length documentaries off the native files, without any transcoding. In premiere just lower the resolution on the bottom of your source/record windows and you're good. For red footage I usually lower it to 1/8 or 1/16 and have edited alot of projects like that.

The only viable reason to transcoding would be to give you some more headroom in the color grade, as 10-bit files have a little more adjustability in their color space. As long as the footage was shot well (Exposure and white balance is correct) you do not need to transcode for color grading. If you are dealing with alot of bad footage that needs fixing, then prores could help a bit. Just transcode the timeline when you're done, this will save you from transcoding footage you'll never use.

I edit on a 2010 full spec'ed out imac and it still runs great, mostly because it still have a decent graphics card and processor. You're laptop could probably do it if you maxed out the ram and swapped in an ssd. Then hook it up to an external display and bam you should have what you need to get the work done. I edited my first features on a 5 year old 13 inch macbook pro and it was slow but got the work done. Rendering was no fun, but it got done.

If you're editing in PP and you're on the latest version, you can tell PP to automatically generate proxies for you. There are several tutorials about doing that, and it works really well. It's not transcoding to Prores (unless you want it to), but you can specify the transcode size and codec.

I just edited a 4k narrative project and I used the built-in transcoding to generate 720p proxies. PP uses Media Encoder to make the proxies while you're still able to edit, and it automatically links them for editing (hint: you do have to manually switch to the proxies when they're generated, but it's a one-button process), but it will automatically relink to the full-size files for exporting. Check it out - it's fantastic for my 2012 Macbook Pro laptop.

Like Michael said above me, PP has an integrated, mostly transparent proxy workflow now. If you notice the system bogging down, click a button and viola, you're working with lower res files and a simple toggle lets you switch back and forth for final rendering. Let it run overnight or work while its transcoding in the background. Depends on your system. Besides any bugs that invariably will crop up, it can't get any easier than that.