My issue with this justification is that these entries aren't restricted to mental or emotional instability of the Mega Evolved Pokemon, they describe active Physical harm coming to them simply as a result of taking the form. I will share some below, excluding any that are touted as speculation such as Moon for Mega Aerodactyl. (Note that some species like Audino and Gardevoir lack Mega Evolution Dex entries, also the ones that involve the least drastic Physical morphing hm suspicious)The way I have always seen it is that what SM describes is what happens when a Pokemon Mega Evolves in the wild or without the assistance of a bond between Trainer and Pokemon, and why Mega Evolution both cannot occur naturally in the wild and why even when a Pokemon Mega Evolves, it cannot stay in that form forever and will have to eventually revert back after a certain period of time.
Gyarados
Ultra Sun: Mega Evolution places a burden on its body. The stress causes it to become all the more ferocious.
Heracross
Ultra Moon: A tremendous influx of energy builds it up, but when Mega Evolution ends, Heracross is bothered by terrible soreness in its muscles.
Houndoom
Ultra Sun: Its red claws and the tips of its tail are melting from high internal temperatures that are painful to Houndoom itself.
Tyranitar
Ultra Sun: Due to the colossal power poured into it, this Pokémon's back split right open. Its destructive instincts are the only thing keeping it moving.
Garchomp
Sun: Excess energy melted its arms and wings, transforming them into giant scythes.
Sableye
Ultra Sun: Bathed in the energy of Mega Evolution, the gemstone on its chest expands, rips through its skin, and falls out.
Sharpedo
Ultra Sun: The yellow patterns it bears are old scars. The energy from Mega Evolution runs through them, causing it sharp pain and suffering.
Glalie
Sun: The excess energy from Mega Evolution spilled over from its mouth, breaking its jaw. It spews endless blizzards.
Moon: It envelops prey in its mouth, freezing them instantly. But its jaw is dislocated, so it's unable to eat them.
Ultra Moon: The power of Mega Evolution was so strong that it smashed Glalie's jaw. Its inability to eat very well leaves Glalie irritated.
Salamence
Ultra Sun: The stress of its two proud wings becoming misshapen and stuck together because of strong energy makes it go on a rampage.
Ultra Sun: Mega Evolution places a burden on its body. The stress causes it to become all the more ferocious.
Heracross
Ultra Moon: A tremendous influx of energy builds it up, but when Mega Evolution ends, Heracross is bothered by terrible soreness in its muscles.
Houndoom
Ultra Sun: Its red claws and the tips of its tail are melting from high internal temperatures that are painful to Houndoom itself.
Tyranitar
Ultra Sun: Due to the colossal power poured into it, this Pokémon's back split right open. Its destructive instincts are the only thing keeping it moving.
Garchomp
Sun: Excess energy melted its arms and wings, transforming them into giant scythes.
Sableye
Ultra Sun: Bathed in the energy of Mega Evolution, the gemstone on its chest expands, rips through its skin, and falls out.
Sharpedo
Ultra Sun: The yellow patterns it bears are old scars. The energy from Mega Evolution runs through them, causing it sharp pain and suffering.
Glalie
Sun: The excess energy from Mega Evolution spilled over from its mouth, breaking its jaw. It spews endless blizzards.
Moon: It envelops prey in its mouth, freezing them instantly. But its jaw is dislocated, so it's unable to eat them.
Ultra Moon: The power of Mega Evolution was so strong that it smashed Glalie's jaw. Its inability to eat very well leaves Glalie irritated.
Salamence
Ultra Sun: The stress of its two proud wings becoming misshapen and stuck together because of strong energy makes it go on a rampage.
So Gen 7 is clearly running with this idea that regardless of controlling it, the act of Mega Evolution is supposed to be extremely stressful or painful to the Pokemon on a Physical level. Not to mention several entries reference the Mega Pokemon turning on its trainer, which doesn't inspire confidence these are exclusive to unbonded Pokemon
Gengar
Ultra Sun: It tries to take the lives of anyone and everyone. It will even try to curse the Trainer who is its master!
Banette
Ultra Sun: Extraordinary energy amplifies its cursing power to such an extent that it can't help but curse its own Trainer.
Salamence
Moon: Mega Evolution fuels its brutality, and it may even turn on the Trainer who raised it. It's been dubbed "the blood-soaked crescent."
Ultra Sun: It tries to take the lives of anyone and everyone. It will even try to curse the Trainer who is its master!
Banette
Ultra Sun: Extraordinary energy amplifies its cursing power to such an extent that it can't help but curse its own Trainer.
Salamence
Moon: Mega Evolution fuels its brutality, and it may even turn on the Trainer who raised it. It's been dubbed "the blood-soaked crescent."
I'm not a conspiracy theorist to the extent of "they made Mega Evolution a bad thing so people would like the new gimmick," but it's moreso an extension of my dislike for Alola's Pokedex entries, which read more like something from an edgy "what if Pokemon but things die?!" fanficition than just a more brutal take on Pokedex entries: compare Goodra or Drampa, which bring up their dangerous strength but also make a clear distinction that it happens when they're actively wronged, rather than just existing or doing something they encouraged barely 3 years prior.