Zygarde's ability, Power Construct, scales his HP in a way that is very different from how the ability is actually supposed to work. It scales his HP in direct proportion with the new HP stat, leaving him with the same percentage of his health remaining as when he transformed. This is not how the ability should work. Zygarde's Power Construct ability simply carries the amount of damage Zygarde took over to his new form. Any new HP he gains as a result of having a higher base HP stat is added to his current total. This leads to a change in the proportion of his HP Zygarde has remaining, creating a "healing" type effect you observe when Zygarde transforms.
For example, I tested it like this. I used a Level 100 Zygarde with 13 HP ivs and 12HP evs. This leaves him with 342 HP in base form.
I had a Landorus-Therian use earthquake on Zygarde, reducing him to 110 HP. Note, before transforming, Zygarde is missing 232 HP. This is just about 32% of Zygarde's health remaining, causing power construct to activate. Zygarde's max HP is now 558, and his current HP is now 179. This is still 32% of his maximum HP. However, Zygarde is now missing 379 HP. That extra damage has come out of nowhere. According to how Power Construct is actually supposed to scale health, Zygarde should have 558 - 232 HP. This comes out to 326 HP, which is actually now 58% of his maximum, which would create the "healing" effect that you see when power construct activates in the main series. As you can see, this cripples Zygarde significantly, as he is left with almost half the amount of health is supposed to have. All of this can be verified on pokemon showdown, as well as by checking the bulbapedia page here. https://bulbapedia.bulbagarden.net/wiki ... t_(Ability
To sum it up, Power Construct scales Zygarde's remaining HP directly to his new base stat to conserve the proportion of HP he has remaining, but this is not actually how Power Construct is supposed to function, and it leaves Zygarde with significantly less HP than he should have when he transforms.
Apologies if I missed anything, and thank you!