After an erratum, Twinned Spell metamagic says:
To be eligible, a spell must be incapable of targeting more than one creature at the spell’s current level. For example, magic missile and scorching ray aren’t eligible, but ray of frost and chromatic orb are. [PHB, pg. 102]
So Twinned Spell metamagic cannot be used with an Area of Effect spell, even if it has only one target, because if someone else were present, they would also be targeted.
The Shield Master feat, on the other hand, says:
If you aren’t incapacitated, you can add your shield’s AC bonus to any Dexterity saving throw you make against a spell or other harmful effect that targets only you. [PHB, pg. 170]
Because this doesn't talk about the spell's ability to target multiple creatures, but rather only asks whether or not someone was the only one targeted, does that mean that a different interpretation applies? If someone is the only creature in the Area of Effect, does that count as them being the only target, even though the spell (or whatever it was) did target an entire area?
AncientSwordMage has identified a relevant question: Which spells trigger the second benefit of Shield Master?
That discussion also references another related question: Does Shield Master only grant DEX save bonuses vs. single-target spells?