Every match win is worth points equal to how deep that round is: a 1st Round win is worth 1 point, 2nd Round 2, 3rd Round 3, Semi-Final 4, and winning the Final is worth 5. A beer's all-time points are simply every one of those added up, across every year it's competed - so consistently going deep matters as much as winning it all once.
Plate competition wins (the wooden-spoon knock-out for 1st Round losers) count too, but at half weight, since it's a consolation bracket rather than the main event.
Points add up per round won, not just for the final result - so a beer that wins every round on its way to lifting the trophy in a given year scores 1 + 2 + 3 + 4 + 5 = 15 points for that one tournament, not just 5. That's why Points per Tournament can come out higher than 5: it's an average across everything a beer won on the way through the bracket, not a score capped at what the Final alone is worth.
# of Tournaments won't always equal R1 L + R1 W for a beer - some years a beer gets a bye straight through to Round 2 (most often when a tournament's field doesn't divide evenly into first-round matches), so it's credited with that tournament but has no 1st Round result to show for it.