In many cases, they have a loft with more sleeping room. When I had family come to visit, we made use of a monthly mansion - it had a single bed on the ground floor, and another single bed up in the loft. I doubt you would have too much trouble with getting an extra bed or futon. The biggest problem is that some of these places (actually, a lot of them) use a hard design plan. The furniture is built into the room. There is a specific spot for the bed, and as it is part of the room there is no way to just move it out of the way and put a larger bed.
There is one thing that does worry me a bit with your plan - when my family was looking around (or rather, when we were looking around for them), unless the monthly company was accustomed to renting to foreigners (which means they tripled their prices) they required a Japanese cosigner of sorts. We ended up just renting it for them, as it was a lot of trouble.
Anyway, here is a list of a few more sites you might want to check out;
http://www.leopalace21.com/
http://www.702622.com/
http://www.good-monthly.com/
http://www.mrb.co.jp/
http://www.monthly-sstyle.jp/
http://www.apamanshop-monthly.com/
And this is one that is dedicated only to Kyoto -
http://www.monthly-kyoto.com/