As Clinton said, it's all about "Arithmetic". You seem to agree with a 20% figure for minorities and suggest that 3% of them were in present day Pakistan. That leaves 17% in what is now BD. Considering that Pakistan was divided into two, the 17% of the total population should have become 34% or thereabouts when the country was halved. The 3% should have become 6% in what is now Pakistan. See the problem?
If you suggest that west Pakistan alone (separated) had never more than 3%, the corresponding figure (to make up 20% of total population) in BD should be even higher.
You got it dude! I guess they don't teach 'rithmetic in Madrassas in Pakistan!