We had to leave early to catch a flight, so the check out time of 9am was no problem for us, but I can see how it would be an issue if you had later onward travel. And because of this check out time, the cleaner walked in at 7.20am, but luckily we were up and showering. Just make sure to leave the "do not disturb" sign on the door! And I'm sure the hotel would hold any bags for those with late onward travel.
We stayed here for one night after a 4 day trek to Machu Picchu. Our room was really comfortable and big, and also quiet. The bathroom an absolute heaven after our trek (hot shower, soft towel, toiletries etc). WiFi was also good and I don't understand the negative comments about breakfast - there is hot and cold food, fruit, cereals, tea, coffee, juices, yogurt - a feast! Also they let us leave our big bags there for the duration of our trek, even though we our night's stay with them was after.