@vitor First thank you answering my question.
I don't think line-height should be considered an intrinsic property of the font, as it is part of CSS as well as iOS font styling.
The Alfred screenshot alone might not be persuasive enough, let me compare the Alfred font line height, with the Spotlight font line height.
As you can see, Apple's Spotlight controls the line-height, such that the search box can look very compact.
Although adjusting the bottom spacing would Allow the search box to be vertically centered, it would make the box super tall, which is not visually pleasant either.