Although the movie's director seems to be under the impression that Pikachu's voice is different from Harry's voice, the novelisation (based on the script) indicates that Pikachu and Harry speak with the same exact voice. This at least confirms that the voice that Tim wasn't recognising was his father's own voice.
For the record, the voice reminds him of a TV detective, suggesting that he's been sufficiently estranged from his father to simply not remember what his voice sounds like.
"I know you can't understand me," the Pikachu said slowly in a
surprisingly deep voice, kind of like the detective from the movie
that had been playing. "But put down the stapler, or I will
"Did you just talk?!" Tim exclaimed.
He was so
shocked, he dropped the stapler.
Detective Pikachu couldn't believe it, either. "Whoa! Did you just
understand me? Wait—wait, wait, wait, wait. That is heavy eye contact
right there. You heard me." "No, no, no. No, no, no. Stop, stop, stop,
stop!" Tim shook his head, refusing to believe the impossible—that he
could actually understand a Pokemon. "Yes, you did! This is amazing,"
yelled Pikachu, excitedly. "You can understand me, I’ve been so