I realize this post is over a year old, but I found it while Googling "cleaning fees for STRs." If you've resolved this by now, I'd like to know who you did. Honestly though, I think you are making a mountain out of molehill.
Sounds like you have 3 listings, i.e., 3 separate bedrooms, in 1 shared apartment (or codo, house, etc.), correct? I have a similar arrangement with 2 listings in my 3-bedroom house: One bedroom is mine, and and other 2 I rent on Airbnb. I do charge a modest cleaning fee, but very modest. I do my own cleaning, so there's no need to to hire a cleaning service.
If you're hiring a cleaning service to clean between bookings, why not arrange with the cleaning company to clean the rooms that need to be flipped, and touch-up the common areas as needed? If having cleaners on the dwelling while other guests are there is a problem, perhaps communicate with guests and in your listing that you have routine cleanings regardless of their length of stay, not unlike hotel service.
Frankly, if hosts are going to have complex listings, I don't think it's Airbnb's responsibility to create fee schemes for very short vs. semi-long-term stays. Sure, the technology might exist, but I think it might be confusing to new Airbnb hosts to figure out, and makes the whole listing listing process unnecessarily complicated.
If cleaning for longer-term guests is too cost-prohibitive, don't offer long-term discounts and decide for yourself what's the longest you'll go without losing revenue from cleaning costs. For instance, if you don't want to go more than 1 month without cleaning the room at least twice, have a 30-night max. On one hand, you'll have a solid block of 30 nights booked, and you might be able to absorb 1 extra cleaning, as opposed to a series of shorter stays and multiple cleanings throughout the month. Longer stays offer more guaranteed income and less work between bookings.