Yes that is my point, rankings do not always dictate the outcome of a particular series, and that is why the H2H record doesn't necessarily mean that the team that won is the better team. It is quite possible for some teams to play better against certain teams.
Hypothetically, Pakistan might beat India in a series, but India tends to outperform Pakistan against most teams, and that is why they are consistently ranked higher.
Performing better against a variety of opponents results in a higher rank in the long-term, which determines who the better team is. India does not have to beat Pakistan to prove that they have been the better team for a long, long time, simply because they have done better than Pakistan overall.
The GoI and BCCI seem content with isolating Pakistan cricket and denting their revenues, which seems to give them more satisfaction than improving the H2H record.
I don't blame them though, we would probably have done the same to India if we had the power and the influence to harm them.