The distinction matters for cases where you want to use huge piles of existing .NET code, sometimes written in other languages. VB.net and F# already have partial functionality in JSIL without any dedicated support, and there's a partially functional MonoGame port that only took a small amount of fiddling. You could of course manually port all that stuff over to Saltarelle-compatible C# (and get great results!) but it's a different approach.
EDIT: One other distinction is that the .NET translation approach results in broader feature support. JSIL supports features Saltarelle may never support, like pointers and structs.
https://github.com/OurSonic/OurSonicSharp/blob/master/OurSon...
maps to
https://github.com/OurSonic/OurSonicSharp/blob/master/Output...
As a bit of self promotion, if anyone is interested in helping on this project, or any other web based c# -> js game, shoot me an email dested@gmail :-)