SCYSA and backbone may not said in the same sentence. I am with you, if they write in then everyone will have agreed by default when competition starts.
To me it is simple. The higher seeded team in R3PL takes #1, in the case where all games in R3PL have not been played, then the higher seed in R3PL at the time when the Challenge league season ends (including any make up dates)is the #1 seed.
If the teams did not play equal opponents then tough it happens...