In the texture.tex file for PBR parameters should we use Alpha=name or not? I have used both. Below is a test, car and cube on right have Alpha= anf the car and cube on the left do not. Looking at the cars I can get the look I am after ether way.
I started writing a long winded reply and then realised I wasn't convinced that Blender correctly identifies the purpose of each texture in, say, a PBRMetal material. A normal texture is obvious because the texture.txt says it's a normal texture. But, if you include an "alpha=" in both the albedo and parameter texture.txt files then it isn't obvious at all which is which unless I've forgotten something which is possible.
The only safe way is to use a mesh metadata file but they can tedious to make if you have several meshes.
I'll have another look at the Blender FBX exporter when I can but it won't be for a few weeks.
Sorry, I haven't answered your question but I wonder if there is more to it than just the "alpha =" issue.
If you do not specify the Alpha= the game automatically assumes the metallic is 100%. Obviously this is not desired in every application, and may even become faulty later, so it's better to add it. In your test example the alpha of the parameter is not pure white and therefore does not give you the same result as the text example on the right, which assumes is 100% metallic (pure white alpha).
Any time you use an alpha channel (whether it's an actual alpha channel or a separate bitmap), you'll want to use the alpha= line, and have it point to the texture with the alpha data.
For pbrmetalmasked; your albedo texture.txt should have the alpha= (whatever) line
If your material has a height map, your normal texture.txt should have the alpha= (whatever) line
The parameters texture.txt should always have the alpha= (whatever) line, as the metallic channel isn't optional.