for fresh chilis, I alway roast them because it lets you get the peel off of them. that reason alone is worth it in the final product.
as for flavor, roasting will consentrate the flavor and thus will impact the final product to some degree but with any long simering dish, that effect is somewhat mitigated.
I say roast away!
as for the tomatoes, you can just use boiling water to get the waxy skin off of them. it is much more easy than roasting.
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