As I recall reading, Factorio a couple of minor versions ago (0.17.28 or so?) added a new attribute on recipes to only show them in the machine that they are applied in and not in the user menu, combine that with putting them in their own tab or at the very bottom of the existing tabs and the recipe lists stay clean. Though maybe that was being discussed rather than added yet... (EDIT: Hmm, can't find it, maybe ignore this paragraph...)
Or could do what mods like WSF do, put all those special recipes in a certain category for a given machine and just hide/unhide them en-bulk when an appropriate building with the appropriate crafting list is opened or closed via the gui open/close callbacks.
Honestly I'd be fine with them all being at the very bottom of the appropriate tabs or just in their own tabs, I always find recipes by searching anyway.