Player rating for tournaments across all installments of Heroes.

But let's talk about the situation where these two Tournaments are played on the same version of the game, and both leaders in both Tournaments participated. The disadvantage for them disappears.

IF all participants always participate in all Tournaments, then yes.
But firstly, this is practically impossible, and secondly, in this case, you can use your first system - there will be no disadvantage.

Let's assume that there is also Tournament 3, where neither A nor B played, but Player C played and, with a result of 1000 days on a super-easy map, receives 100 points according to my first system, just like players A and B in their Tournaments 1 and 2.

Let's assume that there is Tournament 4, where player A and B do not participate, but a beginner player participates and completes a super-easy map in 1 day and receives 10000 points. And for the first Tournaments, where player A and B completed a super-hard map in 10000 days, they receive 1 point each. The result is unsatisfactory.

P.S. In your first system, the same rating was given for all Tournaments, while in the second, a higher rating can be given for an easy Tournament than for a difficult one. Draw your own conclusions.