The .mov exports are huge
what codec are you using? Animation will create large files but will render the fastest, opposite to a PNG codec container.
if the quality is hindered at all by exporting png sequences instead
No, actually Png sequence even allow you to export your video as 16bit per channel which can give you higher dynamic range in grading your image.
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You need to take some time to learn about formats, compression and standards. There are formats and codecs that are sometimes referred to as a Mezzanine Codec or Format that you should be using for your DI (Digital Intermediate). Most of my work needs to maintain color depth higher than 8 bit and i have my favorite formats. One of the best 10 bit formats available is the free Cineware Codec from GoPro, and it even supports alpha channels. I also use image sequences for a lot of my work. Here's my basic rule of thumb. If my AE comp is going to take longer than about a minute per frame to render I always render to an Image Sequence because it's easier and faster to go back and fix 10 frames that the client wants changed. If I have any worry that the render may crash or fail because I have either had problems with the comp or I'm using some effect that I know is a real system hog I'll render an image sequence because it's easier to fix things that go wrong with a render when you don't have to re render the good frames you already have. Most of the time I render to my favorite DI and most of the time this is a .mov format. I try to avoid any formats (codecs) that will require any rendering in Premiere Pro or the NLE of choice for my client. I also avoid 8 bit formats like Animation Quicktime or the Windows Lossless default unless the shot is extremely simple and I'm sending it to someone that has not set a defined workflow.
I hope this helps. I would guess that most of the folks producing video now have little or no understanding of formats, compression or video standards and that is just about the most important basic ingredient in the recipe.