OK, for those that don't know, but (also) want to:
They are perfectly aware of each other. I did a run last night with both enabled, and indeed the timer is reset after all AF runs, and the ΔT is always using the last AF run as reference, regardless what triggered it. The attachment has the relevant snippets from the Log, for the curious.
The only small glitch was in the beginning. I had also set AF after filter change. When I started the sequence, it first detected that the last AF had been more than 4200s ago, and did an AF. Only then it switched the filter, and immediately ran an AF again
Not sure if such a situation could be captured somehow.
But that was really only a tiny irritation. Apart from that it was an absolutely smooth run (including an automatic meridian flip). EKOS is really constantly improving. Thanks to all that make this possible