I propose to add
extensions.enabledScopes = 5
to default preferences for new profile.
Purpose is to isolate FirefoxPortable from running environment a bit and load only extensions form user profile or those associated with application.
In practice: this will restrict searching for exts to paths:
{FirefoxPortableDir}\App\Firefox\extensions
{FirefoxPortableDir}\Data\profile\extensions
while excluding exts listed by registry or located in appdata profiles for current and all users.
More on scopes (no anchor, search page for "Installation scopes" header)