There are a couple of explanations for the presence of tobacco leaves in the mummy of Ramesses II. The mummy had some rough treatment before it was finally examined.

Bucaille, Maurice 1990 Mummies of the Pharaohs. Modern Medical Investigations New York: St. Martin’s Press.

pp. 186-187 “when it comes to interpreting the various samples taken from the mummy, we should bear in mind the mummified body’s history. The following is a brief summary.
The body was buried over 3200 years ago in the Valley of the Kings at Thebes. In spite of the precautions taken, it was the prey of tomb robbers. In all likelihood, the precious objects and items of jewelry that were placed in contact with the body have disappeared. Violations such as these led the priests of the Twenty-first Dynasty, roughly two hundred years later, to remove the royal mummies to a safer place, thus repeating what they had done for Pharaoh Pinedjem. The priests of Amon did the best they could to repair the damage, and once again they swathed the mummified bodies in wrappings. The mummy of Ramesses II was treated in the same way and finally removed to the hiding place at Deir El Bahari near the Valley of Kings. It was there that it was discovered in 1881. Even here, however, the royal mummies were yet again subjected to the violations of modern thieves. The mummy was transferred to Lower Egypt, where most of its wrappings were removed in 1886. Unfortunately, its misfortunes were not yet over. The mummy was mishandled, stored in various places, and even exhibited in a standing position. Finally, it was removed to the Egyptian Museum in Cairo, where it remained until coming to Paris.
It is clear that whenever anything is found that is foreign to the actual body itself, either on the surface or inside the mummy, one cannot attribute it either to the first embalmment or the second treatment carried out by the priests of Amon restored the body. The moment we know that tomb robbers or pollutants may have introduced foreign bodies into the mummy, we can no longer affirm that such bodies date back to ancient times.
After the wrappings were removed 100 years ago, the abdomen was left gaping open at the evisceration orifice. Therefore it was no longer possible to attach any importance to the presence inside the abdominal cavity of whatever material was found there, since the material could have come from the surrounding environment. This accounts for my surprise upon hearing the Museum of Anthropology declare that the morsels of tobacco in the mummy’s abdomen was proof that the ancient Egyptians were familiar with the plant long before it was introduced in the West. I am not disputing the fact that a fragment of vegetation was identified, but it seems impossible to me, even if the fragment was found adhering to the resins of the body. to state that it was introduced in ancient times.

The article you cite, as a matter of fact, discounts the validity of the claim for antiquity of tobacco with a different explanation.

Buckland, P. C. and Panagiotakopulu, E. 2001 “Rameses II and the Tobacco beetle,” Antiquity 75: 549-556

p. 552 “As an albeit unusual stored product, mummies are liable to insect infestation at any point after entombment or exhumation (Panagiotakopulu in press), and Steffan (1985: 112) does raise the possibility that at least Thylodrias contractus may have entered the body after 1882-85. Panagiotakopulu et al. (1995) have discussed the evidence for the use of natural insecticides in antiquity and modern museum wage a continuous war against the damage caused by a wide range of insect pests (Florian 1997). Loti’s comment on the state of Rameses’ mummy shows that the Cairo Museum was no exception. The mercury bath, which he notes that the mummy was subjected to, used a substance widely employed as an insecticide on animals at least since the early 19th century. Kollar (1840) suggests that ‘rubbing with quicksilver would undoubtedly be the most speedy and effectual [sic] for killing the lice.’ He provides a further clue to the interpretation of the evidence from Rameses and other mummies: ‘It is usual to begin the washing with a decoction of tobacco-leaves in a strong lye (also a very effective remedy against fleas in dogs).’
. . .
Faced with an extensive infestation, it is not surprising that tobacco dust was used either in the late 19th century or early last century in the conservation of Rameses’ mummy.
. . .
p. 553 “The use of natural substances as insecticides has along history (Panagiotakopulu et al. 1995), and it is possible, as noted by David (1992: 2000) that some plant materials were used for this purpose in the mummification process. Huchet (1995) suggested that the tobacco from Rameses II was used in antiquity for its insecticidal properties, but we would argue that it is more likely to have had a recent origin during conservation. A similar explanation is likely to account for the nicotine in the Munich mummies examined by Balabanova and her colleagues. The history of the specimens is not indicated in most papers, but the material was clearly fragmentary, including seven heads, an incomplete body and one complete example (Balabanova et al. 1992) The bet documented mummy, examined by Parsche & Nerlich (1995), had been purchased by the Bavarian Academy of Science in the 1820’sw from a Dr. F.W. Sieber of Prague (Dawson & Uphill 1995: 391). Radioimmunoassay showed that nicotine was generally distributed through the body, and it probable that this reflects the application of tobacco water as an insecticide during conservation in the 19th century.”
Bernard