I think what you do is try and estimate how long it takes you to clean per square foot, and then do the maths on that. So, it could be expressed as hourly or square foot, but it still comes down to the same thing. I would expect that the client isn't interested in how long you're working - they only want the job done well and cheaply. So, they're only going to see the final price. You're the one thinking feet and hours.
I think the challenge is knowing how long it will take you to clean a given area. This will vary with the sorts sof surfaces you're cleaning, I would think. If you're hoovering lots of carpeted office space and then buffing a big lobby, or if there are a lot of loos to clean or a lot of stairs.
I really don't know how you go about getting this experience without a bit of trial-and-error in the beginning, to be honest.
I clean domestic. I have a rough idea of how long it takes to clean kitchens, baths, and etc., and I take things like number of children or pets into account. But, at the end of the day, it's still a guess to me.
I wish I could give you more help! I look forward to seeing what replies you get from commercial cleaners.