In some cases, the spacing around characters is intentional, especially in monospace fonts. As best I can tell right now, there doesn't seem to be a way to indicate that, yes, the space really is important, and it shouldn't be removed.
As an example, see https://twitter.com/xkeepah/status/1259891701742632971 - a monospace font with glyphs like |, i, 1, etc. are centered (and some others are offset for aesthetic reasons), but this tool removes all of that.