Neither of these statements gives us any insight into what will happen if player A faces player C, but a traditional tournament structure might well keep A and C from ever facing each other.
Federer > Djokovic (well not lately)
Djokovic > Nadal
Nadal > Federer
Everything depends on the draw. Same with the initial choice of dice.
So the solution is to go the rational way and stop believing in ranking if you claim that tennis ranking is based on a mathematical model that has the non-transitivity property. Where exactly is the problem?
Hell I can even accept that player A > B > C > A if each has different skills and specialities that they bring to the table, without trapping myself and others into declaring it's some "paradoxical nonsense". Do we say rock < paper < scissors < rock and declare it's the end of mathematics?
Even in footraces, the competitors still have influence on each other with drafting and late starting and whatnot.