The Steam Deck itself doesn't have an HDMI port, but the official dock does, and that does support HDMI-CEC (support was added to SteamOS a couple years ago). The Steam Deck also does support controller wake from sleep (added in the past year or so); I've actually seen people complaining about their Steam Decks waking up when they didn't realize that feature existed.
And all of the reviews I've seen about the Steam Machine talk about how well both of those features work.
It does not. Source: have a dock. Latest firmware installed from deck. And because the current Steam controller is a recent release, I had to try a whole mess of third party controllers before settling on PS5 controllers because everything else I tried had Bluetooth pairing issues / disconnects as you approached four controllers.
SteamDeck as a handheld is great plus or minus a few nits baked onto the power / battery life choices Valve made. SteamDeck -> TV and SteamDeck -> USB-C KVM are both workable, with caveats. I had hoped we would see the bug fixes you describe before the Steam Machine release. Alas, no.