Has anyone had any troubles recently leaving and coming back to Portugal while awaiting their residency card (post biometrics)?
Not with a U.S. passport. I have been here over the automatic 90-day visa limit, and no difficulty either leaving or entering PT. I flew to US (via UK), and to UK. Flying within EU does not involve a passport check (flew round-trip Lisbon-Naples). Going across by car also does not trigger any checks.
Other passports might yield different results.