To answer my own question, I just learned about the xprop WM_CLASS command. Run in the terminal and then click on the window you're having trouble pinning.
On the, I guess, "readout" next to WM_CLASS, it should tell you the correct name of the window for the purpose of naming the .desktop file in ~/.local/share/applications. In the case of Krokiet the correct name is "linux_krokiet_x86_64.desktop," not something I would have ever guessed. Then the app will appear on the menu with the name "linux_krokiet_x86_64.desktop," however, you can then use the menu editor to rename it to your liking, it pins, and then everything is peachy and the world is forever filled with rainbows and light.
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