On the contrary, in the definition the following is mentioned under clause 10.2: "The National Capital Commission may designate all or portions of real property or immovables as part of the NILM". The Commission may designate all parts of any real property or immovable, in other words it could decide to expand its land mass. That is where it runs counter to the interests of the Government of Quebec.
I understand Minister Pelletier's letter at the time. He was saying that the National Capital Commission should not be granted more authority than it currently has on designated lands. Further, it could expand its territory because it has the right of expropriation. That would therefore directly conflict with the rights of the Government of Quebec.
Of course, if it goes no further than the limits of current lands, it would not be a problem. However, based on the wording we see, the Commission would be granted the power to expand its land mass. That would supercede the authority of the Government of Quebec.