Never had issues with the HTML. Templates sometimes showed comments in dev mode, but in production builds they were stripped and everything minified. I never used Webpack or other bundlers, only the "dumber.js" from their CLI, so maybe was something related to that?
And yeah, probably they monkey-patched arrays and such, but that was just the way of the world before proxies and native signals. The cool part is Aurelia stuck to web standards, and those “weird mechanisms” were basically polyfills, so even old versions still run solid today, sometimes even faster by leveraging native features.