I previously customized HN a bit via my own CSS additions, with the Stylus browser extension. Personally I think that's a more feasible route for personalization than an interface for that on the site itself. However, there's a problem that HN's HTML layout doesn't lend itself to CSS work: you end up describing elements in terms of ‘a div two items down from the one embedded in that thing’, instead of just using classes. Sprinkling around some classes might be something to look at, for providing users the ability for customization. This should be pretty safe. I'd also say that the structure could be more semantic—but that may break browser extensions and similar existing customization.

P.S. I hurried to this thread because I noticed that the ‘collapse comment’ links became larger on my phone and I can finally hit them on the first try. Thanks to whoever did that, sincerely! Though personally I'd encourage you/them to make the link three times wider still, to take away even more effort. Dunno if it's much visual noise to others, but at least I don't think it encroaches on other elements.

Btw, another hopefully-not-controversial change that I would make is to have the post text black, not gray. It's a pretty important element, isn't it? So it should have high contrast and be readable.