Speaking of changes God made in his "administration" or "dispensations" the difference between Leviticus 12: 3 - and also Genesis 17: 11 - and Deuteronomy 10: 16, Deuteronomy 30: 6, Jeremiah 4: 4, and especially Romans 2: 28-29 is one change as part of a remaking or larger change. It is the change God made from that which is physical and literal to that which is spiritual. Interestingly , he made this remaking or big change, from the physical to the spiritual at the same time he began to bring in non-Jews to himself.
"And in the eighth day the flesh of his foreskin shall be circumcised." Leviticus 12: 3
Leviticus 12: 3 is part of that which is physical and literal.
"Circumcise therefore the foreskin of your heart, and be no more stiffnecked." Deuteronomy 10: 16
"And the LORD thy God will circumcise thine heart, and the heart of thy seed, to love the LORD thy God with all thine heart, and with all thy soul, that thou mayest live." Deuteronomy 30: 6
"Circumcise yourselves to the LORD, and take away the foreskins of your heart, ye men of Judah and inhabitants of Jerusalem: lest my fury come forth like fire, and burn that none can quench it, because of the evil of your doings." Jeremiah 4: 4
Then in Romans 2: 28-29 Paul says "For he is not a Jew, which is one outwardly; neither is that circumcision, which is outward in the flesh: 29. But he is a Jew, which is one inwardly; and circumcision is that of the heart, in the spirit, and not in the letter; whose praise is not of men, but of God."
Deuteronomy 10: 16, Deuteronomy 30: 6, Jeremiah 4: 4 and Romans 2: 28-29 are part of that which is spiritual after the remaking in Christ and by Christ.
Literal circumcision was just a shadow, as in Colossians 2: 16-17, of that substance which was to come when Jesus Christ appeared, the "circumcision" of the heart, being born again in Christ, so the soul could live eternally with Christ?
One way of looking at the difference between scripture and dispensationalism is to find out how each deals with this remaking by God which is from that which is physical to that which is spiritual.
But many dispensationalists will answer this by saying that dispensationalism does not advocate circumcision, and in this answer they are staying within the literal mindset. Dispensationalism holds on to that which is physical in other ways, such as in believing that God still honors the Old Covenant physical bloodline and/or still holds to the land promises in the Old Covenant. There are other ways in which dispensationalism holds on to the physical and literal which in the remaking (Jeremiah 18: 4) is revealed to be mere shadows of the substance which is Christ, his Gospel, being born again of Him and his Gospel.