A few comments:

1. MPEG-4 and WebM are not codecs. They are container formats, which are not related directly to video quality. It's true that those two containers have mutually exclusive stream formats available. But that's another issue. (There are, incidentally, containers that allow many different stream formats, such as my favorite Matroska, for instance. WebM is actually a subset of Matroska, BTW.)
2. Your argument that VP9 is an inferior codec fails because you only observed increased filesize and bitrate. The issue is not that of the bitrate per se, but the efficiency, i.e. what quality you can achieve at a given bitrate. You said nothing at all about the actual quality of the two versions in your comparison. Based on the claims about VP9 you cite, one would expect the WebM version to be of higher quality, because it has a higher bitrate, though whether that's really true in that case is unclear; it depends on many factors. That said, it may be difficult to properly evaluate quality; maybe the difference is imperceptible without close comparison. Good, scientific evaluations of these things consist of double-blind experiments with a decent sample of people.
3. "not only is the MPEG-4 file nearly 200MB smaller than the VP9, the WebM video wasn't even reduced in bitrate." Makes sense to me. Higher bitrate necessarily means a larger file, since you can't stuff bits into nonexistent space. The converse is not true, but if you reduce bitrate, and the file stays the same size, that means space is being used for nothing, which is pretty stupid.
4. A slow codec is definitely a bad thing, all else being equal. Just bear in mind that encoding speed depends tremendously on how the video is being encoded. Some options can speed up or slow down the process by a lot, and defaults are hardly standardized. Not to mention, some encoders are just better than others in some ways (none of this is simple). So, the question is: is the comparison between HEVC and VP9 a fair one? Actually, those are formats, not encoders, so the real question is: which encoders are being used? Ones I know of are x265 and vpxenc (libvpx), respectively, but there are others. That's not to say one can't evaluate formats on the basis of how well existing encoders perform, but encoders are always being improved, so it's not impossible for things to change.
5. "Now try to imagine what a behemoth of computer they must have." I don't know just what their process is, but it almost certainly involves vast encode farms (yes, I think it's plural, just like their data storage). With hundreds of hours per minute coming in, it boggles the mind to try to imagine what their hardware is like, but it must be vaguely like that.
6. I agree that encoding multiple times degrades quality. For this reason, I try to keep my video in a lossless format until it's time to upload, so at least the editing process preserves quality. Of course, I usually deal with simple graphics and game captures, rather than camera footage. Noisy real-world video like that may necessitate a bit of compromise.
7. Anyway, about your saying that DTube doesn't encode video, I was tempted to just say it's a completely nonsensical statement. But I think I understand what you're trying to say: that YouTube makes one master encoding at the start of processing, and then encodes the different streams from that master. Meanwhile, DTube directly encodes the original to the 480p format. Is this what you mean? In any case, it's not really correct to say it doesn't encode videos; it does (unless you give it an IPFS hash for already encoded video; I wonder how it handles that now), just more directly. And that does help the quality.
8. OTOH, one can only stream the original if it's in a streamable format, which means (1) something the web browser supports (which leaves out my favored Matroska if it isn't WebM) and (2) a reasonable size, framerate, and bitrate. If not, it may be necessary to download and watch on one's own computer (they should add a download button to make this easier, BTW), or at least wait for buffering. YT has an advantage, in that it encodes to multiple sizes, up to around what the source is (assuming it's not too large), and on playback automatically adjusts based on what the user's network can handle. DTube currently only encodes 480p, watchable but not great. It is nice to have the original available for download, though.