The "sencha build" command is a low-level command that is equivalent in scope to "sencha compile". So if you have a build process based on JSB files and the like, "sencha compile" is the logical upgrade to that.
On the other hand, if you had used the SDK Tools v2 "sencha app build" process previously, then this is the same in Cmd - except that internally Cmd uses the compiler vs the old JSB process. This is the best option in many cases because "sencha app build" automates so many more pieces of the build process.
But if you had not been using that in previous versions, the upgrade from "SDK Tools and JSB files" to "Cmd and app build" is a bit of apples-and-oranges as it were. I believe you will be better off basing higher-level builds on "sencha app build" but it is a bit different than the low-level approach.