The only thing CUDA accelerated in AE was the ray-traced renderer and now that is considered obsolete. AE barely uses the GPU for anything. See this: GPU (CUDA, OpenGL) features in After Effects
Now, some third-party effects (Mettle's ShapeShifter, Red Giant's Universe, Video Copilot's Element 3d, etc.) do use the GPU, but they'll work on AMD cards or NVIDIA cards and are independent of AE's requirements - check whatever plugin you plan to use for their requirements.
Premiere makes lots of use of the GPU, but you'll have to look at their system requirements for which cards work best.
The rendering glitches to which I think you refer have to do with the RAM preview and not final renders.
Apple introduced a bug in Yosemite that makes AE glitch for several frames on the first time through the RAM preview (no matter what version of AE you have). Once the preview loops, it plays through smoothly. Apple still hasn't fixed the bug. But it's not a major bug. It's an annoyance, to be sure, and it's certainly frustrating if you're trying to demo for a client when it's glitchy.
The new version of After Effects that is being released later this spring has completely rewritten how it does previews, so that bug will no longer be a concern.
There are other issues with Apple's latest OS that aren't even related to video editing that I'll not get into here, but I'm very disappointed with Apple lately. Ever since they pulled out of exhibiting at the NAB Show, it seems they've been neglecting the needs of professional users. They took too long to refresh the Mac Pro line and, when they finally did refresh it, it was more to the benefit of hobbyists than professionals in studio environments. And let's not get started on the debacle that was Final Cut X. (Granted, that's been pretty fixed now, but too little too late for most folks.)
I'm not saying this is a bad business choice for Apple - they've seen impressive growth from their consumers with MacBook, iPhone, and iPad. They just posted their economic figures and any company that can make over 10 billion in profits is doing well! I'm just disappointed that they're letting down the one group of people that kept them going before the iPhone revolution happened. If it weren't for professional graphic artists and video editors almost exclusively using Macs, Apple would likely have died years ago.
Now, however, more and more people are jumping to Windows. Windows 7 is rock solid for using Adobe software. I love it. You get more processing power for your money with a PC and several companies are building very quality machines these days. Until Apple makes some changes, I'll recommend a PC workstation over a Mac Pro.
We have Windows workstations where I work full-time and I have a PC at home for doing freelance work, but I have a MacBook Pro for doing stuff on the road. (It's NOT running Yosemite though.)
Does that help?
Apple may call them MacPro, but they are definitely not "Pro" computers. They simply don't care and everyone is just muddling through. CUDA never worked with AMD GPUs in the first place and AE's lack of proper multithreading is not specific to Macs nor are specific CoDec issues. For the msot part you're citing hearsay and gossip without having properly read up on the details, which is why nobody can take your buying decision off your shoulders. Everything you are asking is simply too vague and generic. You could be editing simple YouTube videos and then a MacPro would be just fine, but at the same time you could be doing extensive VFX and 3D work, where it would simply suck...
Hey there, I don't really have any great answers to your questions but I would say that I work on an HP workstation, 2009 Mac Pro, 2012 MacBook Pro and teach motion graphics in a lab full of new Mac Pros. They honestly all run pretty solidly but none of the machines feel so much faster than the others in day-to-day use with the current limitations of AE. I also run Cinema 4D on all 4 computers and see a much, much bigger difference there. The new Mac Pro does fine for most motion graphics-related tasks. Not the fastest thing out there but not too shabby either.
The recently announced update to AE sounds interesting. You might wait and see if it makes the impact on performance that is claimed in the announcement.