As that sentence is written and punctuated, "dispose of and make" pertains to "Rules and Regulations," not to "Territory or other Property. To write the sentence so that "dispose of and make" pertains to "Territory and Property, it'd need to be written as follows:
"The Congress shall have Power to dispose of, and make all needful Rules and Regulations respecting, the Territory or other Property belonging to the United States...."
Perhaps basic English grammar rules that define the meanings associated with commas differed in the late 1700s from what they are now. I really am not a linguistic historian, so I don't know. I do know quite well what to make of phrases and clauses set off by commas given the current standards for its usage in English. FWIW, those very same standards, except for with numbers, apply also to Spanish, French, and even to Mandarin. Based on that, I suspect the structural purpose, thus the meaning correlate of the comma, is likely to be both universal and enduring since that mark's invention.
I'm aware that spellings of certain words have changes, but a change in the meanings tied to punctuation marks is a much broader genre of difference -- likely something above the dialect level and below the language level -- than is mere spelling.