James Williams has some answers and suggestions for you.
Section 6.2 of the Graphing Calculator Guidelines does say no spaces before or after the keystroke Y=, but the examples given on pages 16 and 20 are referring to actual graphing screens, not keystrokes. An example of the Y= keystroke can be found on pages 10 (print) and 11 (braille), as indicated by the post's author, and follows Section 6.2. More examples reinforcing Section 6.2 appear on pages 36 (print) and 40 (braille), pages 43 (print) and 44 (braille), and pages 56 (print) and 57 (braille).
As for keystrokes not shown in boxes, I would say to use the keystroke indicator since GCG 2.1 states "The keystroke may be shown in print text with brackets, a clear or shaded rectangular box, a clear rectangular box with rounded corners, etc." The "etc." leaves wiggle-room here. I would put a note on the TN page regarding how the keystrokes are presented in print. All keystrokes are transcribed within Nemeth switches (GCG 2.2).
In addition, I would offer a caveat to the transcriber regarding the context of the "keystroke," especially if all keystrokes and references to screens in general are fully-capped. From the example given, that last "STAT" might refer to the "STAT" screen and not necessarily a "STAT" key since the last keystroke used in the example was "ENTER." A reference to the "STAT" screen would follow GC 3 and be brailled as it would appear on the screen (double-capped and uncontracted), but not within switch indicators. Samples 1 and 9 show how to treat references to screens within surrounding text. Sample 12 specifically shows the "STAT PLOTS" menu as both a reference in surrounding text and as a screen.
Hope this helps! Let us know if you have further questions.