1. Tom is in the garden. (Preposition phrase functioning as an adjective.)

2. Tom is in the red hat.

Is the prepositional phrase in sentence #2 functioning as an adjective phrase? Can a prepositional phrase following a linking verb ever be adjectival?

Thank you.
There are no adjectival phrases in your sentences. The prepositional phrase in #1 is an adverbial, and the one in #2 is a subject complement.