If mass and matter cannot be created nor destroyed, then how does Mystique get taller or shorter, for example when she
imitates Trask in X-Men: Days of Future Past
Do her atoms and organs simply rearrange themselves? Does she become more dense?
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In her earliest comic appearances, she was limited to shape-shifting, taking on the appearance of a humanoid within certain physical parameters. She could lengthen her bones and change the appearance of her flesh to appear as nearly perfect replicas of anyone she had ever seen.
She was supposedly just moving her physical mass to create a sculpture of her target (though this made no sense because she would end up being hollow or having cells capable of altering their size at will, nearly instantaneously able to "bulk up" in appearance without changing their actual capacities.
Over the character's existence, power upgrades now allow her to shape-change, drastically altering her body's physical characteristics including shape, length, durability, color and possibly even mass.
In the previous Scifi-Stack Exchange Question: Can Mystique CREATE Objects? The canon character received an update to her powers and abilities in the classic Marvel style.
In 2001's X-Men Forever miniseries, Mystique is exposed to dangerous levels of radiation in order to save the life of Toad. The process morphs Mystique's appearance to match her more reptilian physique from the 2000s film trilogy, and boosts her powers so that she can now morph her body into taking certain desired physical traits depending on her situation at the time.
With her revised powers (a classic Marvel "Radiation Accident") her transformations now include powers such as night vision, wings on her back, talons in her fingers, and natural body armor. These powers make more sense since she would be getting them by imitating things already seen in nature. A cat-like eye would have better night vision, for example.
This 'radiation accident' gave Mystique the ability to alter her size and shape in fashions far more drastic than her previous limitations of a humanoid-only appearance between 4 feet and 7 feet tall, WITHOUT apparently altering her mass.
At least, this is how the Marvel Handbook editors wanted to present it. They were inconsistent with the portrayals in the comics, which led to altering her canon abilities to explain away previous inconsistencies.
So they created an event which gave her the ability to alter all aspects of her physical self without any particular limitations including mass. If mass from "some extradimensional source" was good enough for the Hulk, the Thing, She-Hulk, and Colossus, it was good enough for Mystique.
Mystique's powers increased dramatically from shape-shifting to shape-changing.
We have not been given a clear definition of her powers but they seem to resemble the previous canon versions of the character. She does not appear to be able to alter her size and weight beyond 4 to 7 feet, but it would be readily apparent to anyone who grappled her in her shapechanged form, she was not nearly massive enough to account for her physical appearance in size.
Is this an oversight? Probably, with all of the more physically impressive powers, it is often the smallest powers that defy the laws of physics without explanation ever given to them. The "creation" of mass in characters who change size or shape being one of those things taken for granted by writers, editors, and comic artists (and now movie producers).
According to the Official Handbook of the Marvel Universe: (corrections)
Her weight is listed as 120 lbs. (variable). However, Mystique cannot change her weight when she shapeshifts, she merely rearranges it. As such, her weight is no more variable than any person; she gains and loses it through eating, dieting and exercising. Thus, her weight is not variable.
The fully canon explanation would be that if she appears to be more massy (as she grows in stature), it's likely to be a matter of appearance. She may be holding onto the ground or stamping to give the impression of greater weight.
Similarly, her organs have proven to be very flexible. In the latest reboot (post X-Men forever) she is able to flatten herself, Mr Fantastic-style as well as generating machine objects and animal forms. This means that it's quite likely that as she grows or shrinks, she simply rearranges her organs to suit her outward form and she may be able to alter her molecular structure.