This possibility doesn’t undermine the argument. Other things can be made purely of mass and energy. The author didn’t assert that only physical objects are made purely of mass and energy.

The author overlooks that something (physical objects) can lack a feature (being a theoretical construct) even if it is composed purely of things (mass and energy) that have that feature (being a theoretical construct).

The author does not assume that anything has different features. The author cites to mass and energy, which are both theoretical constructs, to conclude that physical objects are also theoretical constructs. The author does not point out any difference between things.

The author doesn’t try to argue that because physical objects are a theoretical construct, they must have some other feature of theoretical constructs. The conclusion is that physical objects are theoretical constructs.

The author notes that many physicists have suggested energy is merely a theoretical construct. But the author doesn’t use this as proof energy is a theoretical construct. Rather, the author simply asserts as a premise that energy is a theoretical construct.