The Sub-surface railway stations regulations remain in force concurrently with the RR(FS)O. This will continue until the Secretary of State is satisfied that there is appropriate guidance in place and it is being applied effectively under the latter, so that an equivalent level of safety is being maintained. If you're a FRA, you need to continue enforcement of this (uniquely prescriptive) legislation as before. The reason for this is Politics (capital 'P' - Westminster-style).
You're right, of course - they forget that sub-surface stations are found in other parts of the UK apart from London, and other FRAs apart from the LFEPA have to enforce the reg's. If you're concerned, I'd suggest that you contact the guys and girls in Transport fire safety at the LFEPA - they'll probably be more than happy to share their latest views on the draft Guidance, enforcement strategy etc.
PS You'll be lucky to see the Guide in November!!