—They run counter to the Protestant dogma of imputed righteousness.—
I’ve mostly gone to protestant churches and I have never heard that taught.
Luther used the analogy of snow on a dung heap to describe what Christ did.
Christ is the snow that covers our sins, but we remain dung.
The Catholic/Orthodox view is that the grace we receive as a result of Christ’s act on the cross cleanses us and transfigures our souls.
This process continues until the Last Judgment when the elect enter heaven. Purgatory/the bosom of Abraham/paradies as Eastern Christians call it will cease to exist at the Last Judgment.
Our prayers comfort the dead as they await the Last Judgment and assist them to enter heaven faster. We don’t know whether a soul is damned or saved, so praying for their souls is an act of charity.
Our prayers merely ask God to show mercy on their souls. It’s God’s decision whether they enter heaven or hell.