You said "Scaling them in ChemDraw distorts them." ie, if you could scale them in ChemDraw, then scaling them in any external app would be a non-issue (And might be worth an email to the developers for this enhancement). But, because you
can't scale them in ChemDraw, that's why you need an accurate scale in the external app you use them in. PowerPoint offers this scale, Keynote doesn't.
Because I haven't used ChemDraw, I was inquiring if the main goal, then, was a way to get these images into Keynote precisely scaled to 75% or 125%. The solution won't be as simple as PowerPoint's (since Keynote doesn't have this feature) but I'd thought that something simpler than manually figuring out the pixel count might be welcome.