Well Brother, God has cleansed our souls, but not our flesh. The soul has been delivered from the "pains" of sin, but not the flesh. This verse came to mind:
1 Cor. 1:29 That no flesh should glory in his presence.
Thanks for your diligent research for us on how the Spirit and the Flesh are different and distinct, which maybe helps understand this verse:
1 Cor. 1:29 That no flesh should glory in his presence.
Maybe this verse gives light into why God allowed it this way.
If "flesh" were to "glory" in God's presence that would be bad, sin, prideful, arrogant, like Satan was.
God's consuming fire might burn us up or cast us out.
Our "flesh" or "indwelling sin" or "old nature" is so horrible to Holy God, that it can't stand in His presense.
Yet we need it to live here on earth. Just like there are weeds, and mosquitoes on earth, it's leftover from the fall.
God leaves all these fallen things in place, so that His Holiness and Glory stand in stark contrast to fallen things, resulting in praise and glory to Him.
Thus we see our indwelling sin, and our soul hates it, but we give God greater glory as we see his daily grace (not just at salvation but daily grace) given to us to have faith in obedience in confession, and God's repeated forgiveness, to see what we are when left to ourselves, our own strength, our own works without grace.
God has the sovereign right to let us sin as Christians. Just as God has the sovereign right to give Grace to undeserving sinners (enemies, blasphemers, idolaters, haters of God) who become supernaturally convicted of sin and repent.
Our sin, confession, and forgiveness, is like a daily echo and reminder of the original Grace that was given to us at salvation. It has a practical purpose to keep us in awe at God's grace, both at salvation, and in daily battles with the indwelling sin that our soul and spirit hates and battles.
Help me test and prove these thoughts from Scripture.