I read that comment as, "rip huge chunks of Bootstrap and jQuery out of it - should be quick"... well I am guessing given Bootstrap design patterns that they used these tools as a core library in-which they built their site around. They may be planning to leverage these tools in the future, or even just want to give themselves the option to... It's an over-simplification. Likely, this site got them to where they wanted to be... a much more modern-looking site without a ton of effort sunk into development.
It's also completely disingenuous to talk about these filesizes in pre-gzip numbers vs. post. When you look at these "optimizations" without taking into account gzip you are looking at a "worst case scenario" that doesn't exist - this site is gzipping it's assets over the wire. The jQuery gripe is more like 33.6Kb vs 96Kb when you look at it through the gzip lens.
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This sort of response (and subsequent defense) is why I would never show my creations here. It's emotionally difficult for me to see such a stable and mature project as Munin accomplish a bit of modernization only to be nitpicked like this. Munin is a great tool.
"Raise a PR" is perfectly valid here when it comes down to it. I think the internet will handle the extra ~100Kb/page load just fine.