Finally figured out the issue I had last Friday with the single flute thread milling!
(if you haven't already you can read about the issue in my previous post)
It turns out the problem was due to the shoulder diameter on the threadmill itself. By default, Fusion360 decides what the width of the shoulder diameter is, regardless of what it should be; however, they do allow you to add the shank and cutting diameter. I looked around for some time, and even went back to the old tool library to see if maybe they had more options to input data into the tool settings, but alas, no.
I was able to fix the problem in a sort of roundabout way; in Fusion360, there is an option to add custom tools called Form Mill's. The basic idea is you sketch out a 2D half of your endmill, then select the center axis where the form would wrap around to create the tool. Huge thank you to @saundersmachineworks for the video on Form tools, made it super easy, and only took a few minutes to sketch and create the custom tool. Now that I had the custom tool I found the pitch diameter offset by taking the thread size 2mm (2mm-0.4 thread), subtracting the hole size, 1/16", and dividing it in half (for both sides) to get the correct number. I then simulated the toolpath and watched it as it cut through the material, and it ran perfectly! You can see above the two tools in video and drawn out, one on the left sketch pad is the custom form tool, and the one on the right is the tool library input one.