City have been suspended from the Champions League and Europa League for the next two years by UEFA after being found guilty of breaching the European governing body's Financial Fair Play regulations.
City deny any wrongdoing and are appealing against the judgement to the Court of Arbitration for Sport.
That has created the potentially embarrassing situation of City lifting the Champions League trophy in the Istanbul final while their legal battle is ongoing.
Pep Guardiola's side beat Real Madrid 2-1 in Spain in the last 16 first leg to put themselves in pole position for a quarter-final berth.
But Ceferin said the Premier League champions are still an "asset" to the European game despite their off-field issues and insisted there would be no red faces at UEFA if they win the tournament.
"First of all, before Court of Arbitration for Sport decides, we shouldn't comment on that," Ceferin told Sky Sports News on Thursday.
"But whoever wins Champions League, it's good. Any club wins, I like it. It's not a problem. I would like to see a fantastic final in Istanbul. That's all I care.
"They are our asset, I respect them, they are our club. I don't want to say that 'now we don't like Manchester City'. We like them, they are our club. But this process is a separate thing, that I don't interfere."
The case could lead to a fierce legal battle between UEFA and City, who are financed by their billionaire owner Sheikh Mansour.
Asked if UEFA was "up" for a fight, Ceferin said: "We are not fighting anybody. We professionally defend our position.
"I don't like that we speak about Manchester City only. We punished five to 10 clubs per season. It's a regular procedure. Let's see."
Ceferin believes it is unlikely the issue could be resolved out of court.
"I don't want to comment but I doubt it's possible," he said.
FFP, with its break-even clause, has been criticised in some quarters because it prevents direct investment in clubs by owners such as that at City from Sheikh Mansour.
Ceferin admits mistakes may have been made in its implementation and changes could be made, but he defends the concept.
"It was established to stop the losses in European football and it was successful. But in the future, I think we will have to adapt it, will have to change some things," he said.
"I don't know if mistakes have been made. Probably, yes, everywhere, mistakes have been made.
"It's not that we are changing something because it's not working but, for competitive balance, probably we would need more and different measures."