Esparc's page

LOAD LIFTER
This set of artificial muscles increases the amount of bulk you can carry while wearing your armor by 3.

Literally says wearing your armor. You can't be considered to be "wearing" something installed in your body.

Note: this distinction is important if your GM likes to catch your characters with their pants down.

I think the main intention of having the option of upgrading power armor was to allow the player to keep the base capabilities of the armor chassis (unique movement/speed/str) intact while still not falling too far behind in AC/slots. Sure you can go to the next chassis, but most of them have completely different advantages.

On another note: heavy armor differences lie almost completely in slots and AC.

The thermal capacitor upgrade doesn't require your environmental protections to be active. This means that if say an Android has it, they could stay in space indefinitely without a suit. Environmental protections has a limit to how long it lasts, the upgrade doesn't.