In the FLP Impossibility paper, why did the authors claim that e is applicable to every E in proof of lemma 3?
The crucial understanding here is the notion applicability of an event in some configuration versus the effect of applying the event to that configuration.
If an event e applies to configuration C, it follows that e applies to all C, where C is the set of all configurations reachable from C (all admissible extensions of C). This is a simple consequence of the model assumptions. If I can theoretically receive e now, and e can be delayed indefinitely, then I can apply e at any point in the future, perhaps having applied e', e'', and so on.
There is a myriad of conceivable scenarios where, in practice, either e will not be applied by the program (because the program counter has advanced beyond the point where this is possible, as per your example) or where the message in e will be rejected by the program because of some other condition (i.e. internal state that forbids the processing of e). An example of the latter is the receipt of phase 1a and 2a messages in Paxos: they may be silently discarded by an acceptor that has already promised a higher ballot number.
Now we come to the notion of effect, which was omitted from FLP. (One of the reasons that FLP is obscure.) Applying e in some configuration does not imply a measurable transition. A process p could conceivably pop a message from its receive queue and discard it immediately. FLP does not forbid this, provided p behaves deterministically at all times and does not rely on the notion of time. Perhaps, p has received some other message m', which has 'locked out' m, so to speak; ergo, the late delivery of m has no measurable effect on p. This is entirely possible.
The reasoning behind FLP is to only induce a contradiction. If applying e to any configuration in C results in a configuration in D, and if we can prove that D does not solely comprise univalent configurations, then we have shown that there is an ever-admissible schedule that spans bivalent states. Lemma 3 does not state that C and D are disjoint: some configurations in C may conceivably be in D. In the case where applying e to some state C' in C has no effect, then C' is in D by the assumption of the lemma.
In summary, applies simply means that an event may be delivered. It does not mean that it is acted upon in a transition-inducing way.