"is anyone else disconcerted that there isn't a more file-by-file way to explicitly indicate whether or not to use soft tabs?"
I fully agree! I came here to ask if this feature is available in Atom, before opening a bug (probably unnoticed among the thousands of currently opened bugs: the price of success!).
My favorite "dumb" editor (SciTE) allows to change the tab settings per file (buffer): soft or hard (and a button to convert the indentations in the file), size of tab (and size of indentation, but that's something I don't want different!).
I don't understand why I can see (and change) the line ending (LF vs. CRLF), but not the tab settings.
Looks like a very basic feature missing from the core.
Note that I am glad there is auto-detection, that's the usual wanted behavior, but sometime it gets it wrong (got tabs in a file indented with spaces), or sometime we just want to override a wrong guess or just need to enter a tab, etc.
I hope this is a future, planed improvement.