Good project-specific labels to GH issues solves the "polluting" problem. The label/tag system is nicely flexible. It sounds like what you really want is neste

Good project-specific labels to GH issues solves the "polluting" problem. The label/tag system is nicely flexible. It sounds like what you really want is nested threads and top quoting and/or interstitial quote/response features? (Arguably what you really need is commonly called a conference.)