Blender3D straight into Unity3D is awesome when it works, but as you note, having multiple versions can get you into weird situations, and that also goes for different versions of Unity3D.
And as @digipaul points out, especially with team or cloud build, exporting as FBX is always a better option, even if it is more clicks each time you update the art. See the first link on Costs below:
Here are all my Blender3D and Unity3D notes:
Costs of using Blender files directly vs exporting to FBX:
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.