The reason I'd want the character to take Supernatural Sense is that it's a sense that the Credenza has no right possessing.
This is magic. The shapeshifter has no right to be a credenza, either.
On the other hand, if the character turned into a fruit bat I would not charge him for flight or echolocation, since those are things that a bat can do normally.
Characters with True Shapeshifting are really good at disguising, but while they are not obligated to take Modular Abilities, that power build is recommended, which I take to mean that if you want to take any "Creature Features, certain Minor Abilities (page 169), Speed (page 178), Strength (page 183), and Toughness (page 184)," then you need Modular Abilities. If True Shapeshifting had the benefits of Modular Abilities, it would have been in the power description, not in the "Options" section: "Options: None, but the Modular Abilities power (above) is recommended." (YS 177).
About the only thing True Shapeshifting guarantees is a bonus to Deceit/Stealth checks, and the "Skill Shuffle" ability from the Beast Change power. True Shapeshifting is essentially an enhanced Beast Change power.
The shapeshifter in this case *should* be spending Refresh to buy Echoes of the Beast to get the echolocation, Fly to be able to fly, and Diminutive Size to be the size of a Fruitbat.
That said, if a GM is generously granting 4 Refresh worth of powers for free, and not obligating a True Shapeshifter to also take Modular Abilities to power their new forms, then yes: I'd happily take the limitation of needing to pay 1 Refresh for a credenza-legal Supernatural sense, in order to get all those other powers for free when I transform into a Minotaur (or perhaps an Elephant), add in Hulking Size, Supernatural Strength, etc., all without needing to pay for them.