Personally, I would use the OpenEXR file-format for all such purposes … or its big-brother, MultiLayer OpenEXR, if I needed to capture multiple distinct “layers” of related digital data.
I would, therefore, capture “one file per frame,” and … file sizes b’damned!
Uh huh. Your first objective, when rendering, is to be very certain that you have captured all of the digital information that was produced all of the renders … without “[lossy …] compression artifacts” and without losing any of the numeric precision of the (floating-point …) data.
(Hey: external disk drives are cheap, and huge. “Splurge.”)
- OpenEXR was defined for this very purpose by … Industrial Light & Magic.
- “MultiLayer” is an extension to that format, which Blender(!) defined and then gave-away to the CG community, as a standard for recording multiple parallel “layers” of related information within a single file. This extension has subsequently become widely accepted.
Eventually, you will wind up with “The (Tah-dahhh!) Movie™” … as a very large directory containing a very large number of very large files, one per frame … one of many such directories that you have made along the way. Each of these files is losslessly compressed. Each portion of a pixel, each bit of data, is "a big (yes…), phat (yes, yes … but precise) Floating-Point Number. Gigabytes of 'em. Terabytes, even.
“So be it. They represent time. Terabytes, I can buy … Time, I cannot.”
Only at this point … when all that time has been spent and you possess all that oh-so hard won digital work product … do you start thinking about file-sizes and compression, as you start to generate the delivery files in this-or-that movie-file format. But of course, “by this point, The Movie™ is done,” and you have umpteen backup-copies of it. :yes: You carefully carried all of the data all the way to this point without losing any of it, specifically so that you could now choose exactly how much of it to compress away as you make the “final prints.” (This print needs to be iMax … this one’s 35mm … this one’s 16mm …)