Well, the number of times you met Scott is stored in constant 0x40D1 (209 in PKHeX).
You will get the following BP:
const == 13 → 4 BP (can you legitimately get this?)
const >= 9 → 3 BP
const >= 6 → 2 BP
else 1 BP
For reference check this: https://github.com/pret/pokeemerald/blob/master/data/maps/BattleFrontier_ScottsHouse/scripts.inc#L169
However the conversations with Scott can still be triggered, there are a bunch of additional flags that get checked after talking to him.