When I try to export a recipe with a secondary output, it only exports one of each stack. I.e. if I tell it I want 6 string, it exports as 1 string.

• Minecraft: 1.12.2
• Forge: 14.23.5.2847
• CraftTweaker: 4.1.20.562
• Artisan Worktables: 1.22.16-126-g90281c1
• Athenaeum: 1.17.4-9-g33cb77c

I'm not able to reproduce this.

Here's my setup:

Here's the output for a shaped recipe:

RecipeBuilder.get("carpenter")
  .setShaped([
    [null, <minecraft:planks>, null],
    [<minecraft:planks>, <minecraft:planks>, <minecraft:planks>]])
  .addOutput(<minecraft:chest>)
  .setExtraOutputOne(<minecraft:log> * 4, 1.0)
  .setExtraOutputTwo(<minecraft:string> * 8, 1.0)
  .create();

I think he meant secondary Ingredients not Outputs.
This

exports to this

RecipeBuilder.get("basic") .setShaped([[<minecraft:log>]]) .setSecondaryIngredients([<minecraft:stone>]) .addOutput(<minecraft:chest>) .create();

It looks like it's not working for secondary inputs. Did you mean secondary inputs?

RecipeBuilder.get("carpenter")
  .setShaped([
    [<minecraft:planks>, null, null],
    [<minecraft:planks>, null, null],
    [<minecraft:planks>, <minecraft:planks>, <minecraft:planks>]])
  .setSecondaryIngredients([<minecraft:string>])
  .addOutput(<minecraft:chest>)
  .setExtraOutputOne(<minecraft:string> * 8, 1.0)
  .create();

Yeah, it's explicitly set to ignore count on those, but I don't remember if there was a reason or what I was thinking at the time. I'm going to go ahead and allow counts on those because I can't currently think of a reason not to.