Why is it all in the kernel?

It's the neologism they use to own the word and define it however they want. The other one is 'harness' that I didn't even click to see what they want it to mean.

Isabelle seems to use classical logic and set theory. Classical logic is often simpler, but when you do the "hard toil" (as the article puts it) of building recursive functions on set theory, all you've really done is to nonconstructively prove the existence of a set of pairs with certain properties. Good luck evaluating such an abstract "existence" with any concrete argument. Whereas intuitionistic logic as used by Coq is more complicated, but that's in part because its notion of "function" is an actual procedure in your computer that can accept an argument and produce a result.

At least that's to the best of my understanding; it's been a while since I have looked at any of this, so feel free to make corrections.

A kernel bug manifests as the kernel deciding that something is a theorem which shouldn't be. The worst case is when it decides that False is a theorem, from which it immediately follows that absolutely everything is a theorem.

The HOL Light kernel (mentioned in the article) is about 500 lines from one file (https://github.com/jrh13/hol-light/blob/master/fusion.ml), and is a very straightforward implementation of a simple type theory (https://en.wikipedia.org/wiki/HOL_Light#Logical_foundations). I'm not so familiar with Lean, but it would appear its kernel is spread over this C++ directory: https://github.com/leanprover/lean4/tree/master/src/kernel.

As mentioned in the article, HOL Light gets away with a lot because it only cares about delivering theorems. Other systems want to retain the proofs as artifacts (sometimes called certificates), and once you do that, you need to make sure these artifacts aren't stupidly huge or otherwise useless. Provers such as Rocq (and I assume Lean) additionally want their proof objects to contain decent executable algorithms backing the proof.

HOL Light also does pretty much no evaluation. The most it understands of evaluation is that (λx. f) x = f. If you want to evaluate anything more complex than this, you build that in "userspace" and you do all the equational reasoning manually via the kernel.

Lean and Rocq kernels do full evaluation of recursive functions, so they have to come installed with an API for building those recursive functions and internal checking to make sure those functions are terminating. The article's author is asking whether you could redo something like Lean and Rocq where the recursive function API was much simpler. I've wondered for a while whether you could also have the evaluator as basic as HOL Light's, and do the rest in userspace. I think there were theorem provers like this that went out of fashion decades ago.

It used to be a much more exciting space before Lean somehow got everyone's attention. The author is the co-creator of Isabelle/HOL, and is still not sure why there is so much more excitement for Lean than for simple type theory.