Well, again--one would have to take a look at the original documents. Really "look".
It would be a neat thing to get all the Law Enforcement "Questioned Document" section (the section that investigates forgeries) to take them under the jeweler's loop and then some.
I certainly agree, but do they still exist? The article at the link says the trail ends with Edwin Stanton: "Historian James O. Hall searched widely for the missing papers and finally tracked them to Stanton. ' Suspicion lingers,' Hall wrote, 'that Stanton consigned them to the fireplace in his office.' No further trace of the original papers was found, and the argument over their authenticity still rages."
In looking at my own personal collection of documents, the embossed seal would be on the document, as well as seals if they were official yet, the etiquette of the day--if the letter was a third party document, it wasn't necessary to seal the letter--this being before envelopes had lick a bit to glue shut. The seal was either wax, wafer or glue--much like rubber cement.
There were lick-em-stick-em envelopes then, and that might actually have made it easier to alter the papers, if they were inside an ordinary envelope, since most could be reopened by moistening them again. Here's an article on envelope-making machines in the period, from The New American Cyclopaedia, 1863, p. 230:
"In these machines the [unfolded] envelopes placed in a pile are brought up from beneath the table by a counterpoise, and the top one is immediately taken up by the gummer, which comes down upon it, and leaves the required quantity of gum in the right place to secure the end and back flap--
the front one, as in all machines, being first gummed by hand and dried. The paper dropped by the gummer is then taken by a carriage under a double plunger, the outer portion of which forces it down into the mould, and an inner part follows, turning over the flaps in succession."
R. T. Knight of Philadelphia (p. 113) apparently tried to remedy the problem by inventing a patent envelope which couldn't easily be unsealed, claiming "It is, for some purposes, quite a defect
in the present envelope that the gum may be moistened and the letter opened without discovery. Wafers may be soaked nearly as easily, and wax is liable to melt in hot climates."
But I'm not sure the papers were sealed or enclosed in anything at all. The article at the link says, "two folded documents and a pocket notebook."