I can't think of any recent professional interaction with a woman (I'm a man) where the mere act of 'asking if she feels uncomfortable' or underlining how this is not a outside-of-work-type situation wouldn't be enough to make the whole thing uncomfortable.

It'd a milder form of saying 'I don't want to have sex with you, just to be clear.'

I'm sure there are situations where this can and should be said, and where this might be done in a non-awkward way, I'm just saying that in many cases it's not that simple. Being explicit can be creepy.