I think you are right about the "why isn't Spy++ changing as I press a key in Chrome", I was getting the same results. Looking at
http://www.bcheck.net/apps/hoekey.htm I see a section for "Keys" and it made me think "You are using a keyboard shortcut, to send a keyboard shortcut", and that is where you may have to approach this problem in a different manner.
The "MSG" in HoeKey is to duplicate those call/wParam/iParam; but those aren't keyboard presses. I think that's why you aren't seeing anything in Spy++.
To fix your issue: does your Extension send a MSG of call/wParam/iParama ? Perhaps you could use those values.
Or: Have your extension instead use one of the shortcut HoeKey does offer with "Keys" like Ctrl+Up, Ctrl+Down, Alt+Up, Alt+Down; but there might be an issue there because I don't see an option in the "Keys" section to specify "I want this keyboard press to be executed in this program"; it seems to just put in the text where the cursor is at the moment.
FYI: Always save before testing, I tried:
~A=Keys|Now is the %g for all good men to come to the aid of their parties
Then ran it in notepad, I saw it type: Now is the
Then the computer locked my account as if I had hit Window+L and when I logged back in a bunch of command prompts were open, with another in the Run box, Notepad was blank, and everything was frozen.