Looking at the SM64 video, he: 1. misrepresents the work from the SM64 decomp project (some of the decomp developers even commented in the video comments); 2. misreads and/or misunderstands the toolchain errata, what he describes in his audio track doesn't match at all what he shows on screen. But there isn't much of a claim to debunk, because it's all hypothesis that "Nintendo wouldn't make such a basic mistake, it's deliberate".
Anyone who has experience working on emulation and reverse engineering of Nintendo games can tell you that Nintendo keeps doing basic technical mistakes when shipping production games. Dolphin's wiki has a whole category for "games that shipped with debug symbols". Pikmin has a freakin' mostly-working PC port of an early version of the game on the GameCube disc. There's also no evidence that other N64 launch titles had the same idiosyncrasy of compiling in -O0, and the whole SDK is compiled in -O2 as he even mentions in his video. How does that fit with the "early toolchain" line of reasoning?
TL;DR: Actually forgetting to build with optimizations enabled is completely in line with what emulation developers and game reverse engineers have seen from Nintendo in the past 20 years. MVG just states his own theory as fact, without the Nintendo console hacking / RE / emulation experience, and with very little evidence which doesn't even match his own claims.
EDIT: See also [1] hidden in the 2nd page of YT comments on that SM64 video, from someone who was involved with the SM64 decompilation project.
[1] https://imgur.com/XZ45IZH