In my experience the two systems are not linked.I used to work at LHR until late last year, although not for AF or any of their handling agents, but the compliance system is uniform throughout LHR as far as I'm aware.
The airline staff can see if you have come through security or not and what time you came through and it's up to them if they take you off at the cut off or not. If you've only got hand baggage then they are not likely to offload you until the last minute anyway, and even if they do and you still turn up in time they can always just put you back on the flight. Just kindly inform them to offload you from the later flight incase they are needing the seat or are waiting around for you.
I would say you've got a good chance of getting the earlier flight even if you just miss the compliance cut off. It was often the case that someone would show as not coming through security, but was in actual fact sitting at the gate. A common occurrence was that someone was arriving in to say, T5 and connecting to say, T2 on separate tickets and only got their boarding pass issued at the transfer desk once airside in T2. The compliance system would have no trace of them passing airside.
As for your other question, I am not 100% sure, but I don't ever recall people being rejected at security because of delayed flights and compliance rejecting them based on the STD. I am sure it works on a rolling time, but if this is automatic or updated by the airport ops department I'm not sure. I know I never had at input on compliance.