Someone who gets a third strike must serve the maximum sentence possible without parole, unless the court considers it would be manifestly unjust.
The High Court judge also granted bail to the pair ahead of their sentencing in May.
Acting Crown Solicitor Anna Pollett did not oppose bail but indicated the Crown would be seeking prison sentences.
Defence lawyer Bill Lawson said he would seek a sentence of home detention for his client Te Whetu, who had "beaten her addiction" and not failed any drug tests while on bail.
He was waiting on a psychiatric report and argued Isaiah's death was caused by an "omission, as opposed to a positive act which caused death".
Roger Laybourn, defence lawyer for Neil, said his client was a "prime candidate" for home detention as the "lesser offender" of the pair.
Neil had no idea his son was in the car, said Laybourn, until he found Isaiah there.
However, Neil did not call 111 and therefore breached his responsibilities as a parent, said Laybourn.
"He should have taken immediate steps to call emergency services."
After the hearing, Te Whetu and Neil, who have two other children together, left separately in different cars.
Neil declined to comment, other than to say: "It doesn't change anything. It doesn't bring him back."
There are no minimum sentences for manslaughter cases, which means judges can impose sentences which differ widely depending on the individual circumstances.
Two years ago, a health professional in Wanganui was discharged without conviction after pleading guilty to the manslaughter of her 16-month-old son.
She accidentally left him in the car in January 2015 and he died of dehydration and heatstroke.
