When a custom tooltip is added to a spawner via CraftTweaker with SilkSpawners installed, the custom tooltip does not appear.

CraftTweaker code used for adding tooltip: <minecraft:mob_spawner>.addTooltip(format.gray("Craft together with a filled morb to change spawner type."));

This is an issue with craft tweaker's if statement returning from the list if there is already a tooltip even if the assigned tooltip hasn't been added yet. It's on their side not mine I don't remove tooltips I add them you can view the source if you want your on silkspawners github.
CraftTweaker/CraftTweaker#532

CoFH Core-related tooltips work fine when changed. The instance that I originally tested the tooltip bug can be found here.

I've also tried it with <minecraft:mob_spawner>.clearTooltip(); before tooltip was added and nothing changed.

Well I add mine via events but, I don't remove anything still not my issue on why it's not showing up

It looks like that any tooltip created with the help of CohfCore works fine with creafttweaker (Thermal Expansion has some really expensive tooltips), so the issue is probably on your side.

Your code is correct, but there might be some sort of minor overlook or something.

@Frontrider look at my tooltip event I don't remove anything. It's not on my side I only added the tooltips. If it was on my side It would have either been fixed in 2 seconds or been purposeful that I was clearing the list.