I think the best scoring format would be points based such as
1: Win: 3 pts. w/1 pt per goal max 3 (promotes subbing)
2: Shutout 2 pts. w/max pts. of 3 goals (again for subs)
3: Tie at end of reg 1 pt. each w/OT goal pt(s) for goals scored in OT. In PK situations pt(s) for each goal max 3
4: Tiebreakers: Goal differential on region opponents, if still tied, Head to Head goal differential, if still tied number of shutouts in region and finally if still tied goals allowed.
In your scenario the 4-1 win would net 6 pts. while the 1-0 nets 5.
Regarding TL.H, maybe they would prefer Clover however I believe they played in a tournament already that went to PKs (where TL.H won) without A. Pantousco or her sister playing. Might have been a game changer (or may not).
Not hating on FM. I have respect for the program (as with ANY program that teaches the "right" way to play). It is a shame that the rivalry between the two teams will not be the same next year and yeah it would be a great final. A nice sendoff.
