Ferrari protege Bianchi sealed the second Marussia seat on Friday when the team had to drop Luiz Razia due to sponsorship issues.
Marussia admitted earlier this week that it was seeking a new engine partner for next season as it did not expect Cosworth to continue.
Analysis: Bianchi a boost for Marussia
But Lowdon said hiring Bianchi was purely about choosing the best available driver.
"Discussions on engines are taking place in our team like every team, but with every supplier," Lowdon told AUTOSPORT.
"This is very much an opportunity to put a young driver in who we think has got a good future."
He acknowledged that developing a link with Ferrari via Bianchi could be a useful avenue.
Ferrari is keen to maintain its customer engine rota and is set to lose Toro Rosso to Renault next year.
Asked if he felt the Bianchi deal could ultimately boost Marussia's chances of a Ferrari tie-up, Lowdon replied: "You would assume it can't hinder them, but it's not central to the thinking behind putting him in the car."
Bianchi was in contention for a race seat at Force India, where he was third driver last year, until Adrian Sutil got the nod on Thursday.
Lowdon said Bianchi's Ferrari background and Force India role meant the lateness of his Marussia deal would be no issue.
The Frenchman will only get one and a half days of testing in his new car before the season-opener in Melbourne.
"It's attractive that he's got a structured background like that," said Lowdon.
"He's clearly quick but also well prepared. Although the season starts pretty soon, I don't think that's going to faze him at all.
"It's useful that he's had some very recent seat time."