Have you checked the headers that these site(s) are sending/receiving? There's usually a couple of indicators in them that point towards whatever tech stack is running.
It could also be the data collected from HackerNews as WhatRuns consider subdomain as part of the main domain.
Most users like to know the full tech stack of a website. If there is a blog at blog.company.com which is using Intercom, it can be a useful data. I hope this makes sense.
Anyway, we will definitely address this issue and consider introducing an option for subdomain separation.
https://www.whatruns.com/website/ycombinator.com
That sounds strange. Can these claims be backed up somehow? I cannot see anything in the source that would confirm these.
It also says Facebook uses Google Analytics \o/