Property rights are rights given to people by their government. Such rights may be restricted to a person personally (Which appears to be the case rights after the Conquest of England by William the Conqueror) or to such person and his heirs (Which is how real property rights are defined in the US today). Justice Marshall did not want to say that all property rights comes from the government, he wanted to say it was an old right and did a long paper say how that was the case. The problem is property rights can be abolished by government or even a change in government. For example In Iraq when the US went in, the US refused to recognize the Chinese claim to oil concessions the Chinese had purchased from Saddam. Why? The US claimed since Saddam was no longer President of Iraq, the US had the right to determined whose property right the US would recognised and refused to recognise the Chinese property right.
The Communists in Russian did the same thing after 1917 (and in the post WWII era in Eastern Europe), i.e. refused to accept pre existing property rights as being valid on the grounds the Communists had not given any such right and the rights given had been made by the Tsar and those rights died when the Tsar was overthrown (or in the case of Eastern Europe, when the Communists overthrew the post WWII government and imposed Communist governments on such countries).
Justice Marshall saw the same thing occurring in France during the French Revolution and wanted real property rights to have a higher claim to existence then a mere product of the Government that issued that property right, but at the same time accept the fact that the Native Americans right to the property was extinguished when the US entered into a treaty with them taking the land.
Since 1823 when Marshall made his ruling, the taking of property during revolutions have become the norm and thus modern jurists are willing to accept the concept that all real property rights come from government, and if the government that issued those rights gives up control of the land to another government, all property rights issued by the first government dies when the first government gives up the land. Thus when the First Nations gave up the land to the US government by treaty, all rights to the land were abolished and any property right to the land is depended on what property right is given by the US Government when the US government sold the land.
This same rule applied to land taken from France, Spain, Mexico unless the US, in the treaties, taking those lands, agreed to recognise existing ownership rights (this occurred in the case of Spanish Land grants in the Southwest and in Colonial America when the British took New Amsterdam as to Dutch real property rights).
Justice Marshall ignored the "War" between Maryland and Pennsylvania over their border, both colonies sold land that the other colony claimed (under the land grant given to each colonial government, Philadephia was in Maryland and Baltimore was in Pennsylvania, the Mason Dixon line of 1763 was agreed upon to end that sometimes brutal fight over who had the right to sell what land).
Side note: One of the leaders of the Maryland claimants to land in Pennsylvania, when captured by Pennsylvania and sentence to be hanged, on the gallows seeing Philadephia said "Yes, this is indeed the greatest town in all of Maryland".
Marshall also wanted to avoid talking about the dual claim to Western Pennsylvania by Pennsylvania and Virginia in the American Revolutionary period (George Washington owned extensive land in Western Pennsylvania, but from Virginia land grants NOT Pennsylvanian land grants, as part of the decision to get everyone to agree to the Articles of Confederation in 1781, Virginia gave up its rights to give such land grants on the Condition the existing land grants to George Washington and others would be recognized by Pennsylvania).
More on the Pennsylvania-Maryland land dispute:
https://en.wikipedia.org/wiki/Cresap%27s_War
The Actual case of Johnson v. M'Intosh 21 U.S. 543 (1823):
https://supreme.justia.com/cases/federal/us/21/543/case.html
Some commentary on the case:
https://en.wikipedia.org/wiki/Johnson_v._M%27Intosh
Justice Marshall avoided the disputes involving Pennsylvania land and land claims from Maryland, Virginia (and Connecticut, which claim northern Pennsylvania during the Revolution) for all were settled on the basis of each state giving up their right to sell land in Pennsylvania if Pennsylvania agreed to recognize land already sold by them in Pennsylvania. i.e. Pennsylvania agreed to say those sales where in effect its sells of those same lands and thus the only real property land was based on the fact Pennsylvania was the Government that 'Sold' or "Recognised" the ownership of those lands. i.e Since Pennsylvania was only government controlling Pennsylvania, land title in Pennsylvania came from Pennsylvania even if technically the land had been sold by Maryland, Virginia or Connecticut.
Justice Marshall wanted some higher right of right to real property then mere power of Government, but the power of Government has always been the sole determination of any property right. When Rome fell and the Germanic Barbarians moved in, the Barbarians rule was based on they ability to determined who owned what property. That is how Rome had determined real property rights and how every government before and since Rome has done so. France had had its revolution in 1789 and that had lead to a massive confiscation of real property in France without compensation and distribution of such land to French peasants. Marshall disliked that taking of real property without compensation and thus wanted a higher right to owning real property then merely saying such ownership right is from the power of the Government, thus Marshall's use of the concept of discovery instead of going with property right is derived from the Government the property is controlled by.
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