2. Using the OS drive for media and cache is definitely not recommended or helping
4. No not with XAVC if using multiple layers or streams.
5. Raid 1 gives realtime data protection. If either drive fails the mirror protects the failure. Raid 1 is to reduce downtime if a drive fails. It's not 100% but it is effective so as long as you have backups then you should be fine.
Although I am a Windows guy, I looked up the specs of your machine and saw a few things :
Most of your machine is very capable, your CPU is an i7 which will give you 8 threads at a good speed....your CPU turbos up on all cores running to 3.9 Ghz , which is pretty good!
Although your NVidia GPU is a MOBILE one, the780M, it is MASSIVELY better than the 765 M I have in my Asus gaming laptop.....you have 4GB of video memory and double the CUDA cores of my GPU. Because your GPU is a 7xx series GPU, you CAN try and "tweak" its performance by using a free program to overclock the " memory clock" of the GPU. You cannot do this on the 9xx series Maxwell GPUs,but, you CAN do it safely with the 7xx series GPUs. On my laptop, I have the same starting frequency as you for the stock memory clock...2000Mhz. I use the free " MSI Afterburner" utility to increase that setting to 3000Mhz with NO overheating....for Macs, there must be a similar program to "tweak" your GPU. These programs allow you to monitor the GPU temperature real time, so that you know you are safe. Your video card, being a moble card, is deliberately UNDERCLOCKED at 2000Mhz in order to save battery power in a portable machine. Both Bill Gehrke and I overclock our cards safely and I get about a 20 to 25% increase in performance when the GPU is "saturated" with effects,or, when heavily used during exports. Especially with an overclock and the 4GB of video memory, your GPU is very good.
You have 32GB of system memory....that is pretty good....make sure that in "settings" for PPro that you have the correct ampunt of memory " allocated" for each core. The minimum is 3 GB per core and you may place more......Eric probably knows the best exact setting for you.....you want to leave a certain amount for "other programs".....what that is for your machine he could say better than me. Make sure all yor machine's "power settings" are set to " maximum performance" so you don't get an unknown "throttling" of the CPU or GPU while the computer is in use.
You are CORRECT that your current drive speed is a DEFINITE "bottleneck" and is probably the cause of your problems, although monitoring the load real time on your CPU and GPU will tell you if THEY are overloaded to 100% usage.
Your " Fusion Drive" is a peculiar combination of a 128 GB SSD and a 7200 RPM hard drive....it operates differently than a "hybrid" drive, where the SSD component acts as a "cache" . Your Fusion drive CAN operate very fast only under certain conditions. Very large video files will be sent automatically to the hard drive portion and then be served up to the editing program in a much slower manner than the SSD portion would do.
So, you NEED to have your footage on a FAST drive and your machine has several options. Some machines, ( like mine from 2014 ), have USB 3 ports that are capable of working with a NEW specification called '"UASP" which allows external drives to run over the USB 3 connection at a speed close to that of an internal SSD. For example, I have a Samsung T1 external SSD that is 1TB capacity, and it runs connected directly to the USB 3 port at OVER 400 MB/second read and write. If my machine did not support the "UASP" protocol, than the performance would drop to about 275 MB/sec read and write. Any data coming off your spinning hard drive and NOT the 128 GB SSD would be travelling at 100MB/sec down to 75 MB/sec under the BEST of conditions. Trying to read and write from that one Fusion drive at the same time will REALLY slow things down. A 1TB T! SSD is around $350 and the 500 MB version about half that, but it runs very fast. A USB 3 "UASP" device may be cheaper, or, may perform faster than a Thunderbolt connected device...I am not sure....you will have to check THAT out very carefully.
The Thunderbolt connection is very fast, even considering the difference between version 1 and version 2.....same with the mini display port connection.
Because quality SSDs have dropped in price, if I were you, I would be strongly tempted to install a new Samsung 850 Pro SSD in place of the current Fusion drive to insure maximum read and write speed of whatever is on that drive of over 500MB/sec. I would THEN make the fusion drive a large backup drive to contain archived work and all archived project files and footage in an external enclosure. However, if you keep everything OFF of your current boot drive that has anything to do with PPro, ( except the program itself), you may be OK with your current drive. You would want to place ALL the footage, previews, media cache, cache , and exports on the fastest and largest external drive that you can afford. The T1 is perfect for this, ( they now have the T3 version), OR, a Thunderbolt device which performs equally fast may serve the purpose.
Once you straighten out your drive situation, your machine SHOULD run better, but again, Eric would know the best as he is very familiar with what the minimum type of hardware is needed to process the different codecs....some codecs are harder than others to process.