Without knowing how their code is written it's almost impossible to know exactly how those situations are handled. Having said that, I'd have to look, but I don't know if I have multiple rules that trigger of the same Whenever statement (I checked, see more below).
My mention about coding above was really to say that I am very careful with how I program rules. As I've mentioned in other threads, I have NO rules that check ever X duration (seconds, minutes, or hours). I haven't found a case where I absolutely need that done, and I have concern of exactly what you're discussing in this thread (e.g. what happens when sunset and every X second occur at the same time). I purposely try to avoid those scenarios.
I just checked, and of the ~65 rules, I have 2 pairs that trigger off the same WHENEVER; Sunset and a motion becoming not secure.
I don't have any issue with any of those firing, but I looked a little deeper for the SUNSET ones. Of the sunset based rules one simply sets a counter, and the other sends messages to turn on some outdoor lights. Neither of them have AND statements attached. The counter of the first, is actually used as a trigger to end up turning on an outlet.
If I ran into a case where I was having an with the second rule firing, I'd simply set a phantom output at the end of the first, and trigger the second rule - which is pretty much what I'm doing above anyway. Since I don't have any AND statements in either line, technically I could just combine the THEN statements into a single rule - one was programmed in 11/2012 and the other 5/2014, and I'll admit that I didn't bother to look through the rules to see if I already had a WHENEVER sunset rule before I created the second.