"I think you would have been good at raising a pet, sir."

Is she purposefully not commenting on the Flerkens? Yes. Definitely on purpose. Because Madoka thinks it's sweet of him to think of her and the other kids on the train, but at the same time, she definitely does not want to think about these Flerkens.. Or be anywhere near them. What kind of creature can swallow stuff that big! That's terrifying, like something out of a horror movie!

But she's worried saying that sort of thing may offend him on some cultural level, so she instead focuses on the latter half of what he says.

Especially since it provides her with an opportunity to compliment him, and Madoka always latches onto those.

"You're really sweet when you need to be, after all."