Phoenix ELN includes material purities into stoichiometric yield and equivalent calculations, if specified. Unspecified purities are assumed to be 100%. 

Here's an example for demonstrating the difference between specified and unspecified purities: Assume you isolate a product in 96% yield, which is fantastic. However it turns out that its purity is only 50%. Specifying the obtained 50% purity in the product dialog will lead to an effective 48% yield, which actually reflects all the product you have at hand - the rest is side products. Not specifying a purity leaves the reaction yield at 95%, which may not fully reflect the quality of the outcome. 

It's ultimately a team decision on how to handle purities for stoichiometric calculations. It's basically the choice between realistic and optimistic calculations, the latter always assuming 100% purities. The important thing is to agree on a common policy to obtain comparable yields with a well understood meaning.