We aren't lawyers, so we can't offer any advice about what's allowed or not. I would point out that the clickthrough license does contain this language (emphasis mine):
2. Restrictions. You covenant not to (i) use the Specification for any purpose not expressly permitted by this Agreement; (ii) use the Specification to develop or make any device, accessory, software, or other product or service available for distribution to third parties...
So I would guess it depends on how "distribution to third parties" is interpreted.
Seems like this could spell trouble for Homebridge - at least the part that implements the protocol (likely not including the Indigo part contributed by webdeck). Homebridge was reverse-engineered to begin with (so what's there now is probably ok), but proving that any modifications from this point forward were reverse-engineered vs gleaned from the spec is likely to be pretty hard (if Apple decided to go after Homebridge). I really hope I'm wrong about this BTW...