Is it better to shade a model inside the 3D modelling software or inside unity?
as an example if I need to use a transparent model should it be made transparent inside the modelling application or inside Unity?
You are asking two different things here, as I can see.
One thing is what you will model, in whatever 3d modeling software you choose. There you will build your model from scratch, define forms, colors, textures and whatever you need. Note that here you will be using the shaders from the 3D sofware.
Once you model is done, you'll export it and import on Unity3D. Here you'll have a good list of possible shaders to be used on your texture. Or you could program your own shader here.
If you are going yo use transparency or not, its a two step process:
I can't define what I'm saying as the best practices, but I can say that is what worked well for me so far.
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