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That's a question for your text editor.

I use Sublime Text 3 with GoSublime and have noticed that the undo stack is just my changes (makes sense, the goimports is an external process), but that's cool because any CTRL+S is going to trigger goimports and so the correction of the imports is invisible and always there.

In Eclipse, this is true. The import was considered an "action" that got put into your undo stack. It was just triggered by the editor, not you.

I believe it has worked well for me for undo. However some other Atom formatters have broken my undo in weird ways, namely the formatter for Node JS I had turned on to auto format on saves. I had to turn it off.