I believe the roots of the “Align to direction” checkbox on this shape module probably lie with the origins of converting right-hand-rule FBX files into left-hand-rule geometry for Unity.
The way Unity did this was to swap some axes and then rotate it to (-90,0,0) at import time.
Circa 2021 or so Unity introduced changes to allow a different approach and I haven’t looked into it.
I’m guessing something like this is happening, which likely makes it “not wonky,” in the sense that some data transmogrification must be needed.
OTOH, if you had geometry in Blender, they ALSO changed how Blender shapes were imported: they began importing Camera and Light objects from Blender (which does absolutely nobody any good anywhere!), but has the pernicious side effect of changing the orientation of any object that was previously solo in a Blender file: by importing object, camera and light, it automatically inserts a parent GameObject above them all, and that is where the rotation for ALL happens, making all the children now wrong, including (perhaps) your particle system.
Here’s a bunch more random scribbles if you wanna read on:
Unity imports Blender3D objects as FBX via a little Python script:
The Python script that Unity uses (substitute your Unity version number or search) to import:
Blender3D objects used as trees / detail in Unity3D terrain (See the second half of this response)
Probuilder and Probuilderize and Blender:
Some more potentially-useful info:
Updating Blender files without breaking your prefabs:
When I work in Blender3D for Unity3D use, I follow these organizational rules:
use Empty Blender Objects as folders: they come out as an extra GameObject
ALWAYS parent everything to a single Empty, even a single object
put as few objects in a given .blend file as possible, combining them in Unity into a prefab
REMOVE unnecessary items (Light, Camera, etc.)
use good names for your Blender3D objects and NEVER RENAME them after Unity sees them
don’t even think about final Materials or Textures in Blender. Set the mesh to use N different materials, but always set up the materials within Unity and disregard what gets imported.