Finally managed to get the command line for the packaging.
-target is set to apk‑captive‑runtime so, everything seems to be fine.
So, I did what I should have done first. Created an empty project in both: IntelliJ and Flash Builder. And both are just fine (same memory usage, etc.).
Maybe the reason is not the compiling / packaging, maybe an ANE or a SWC is causing this (although I don't know if this is even possible).