It seems you have a lot to complain about the systems in Japan!
I'm not sure exactly when you will stay in Kyoto, nor where you will come from, but if it's just BEFORE Golden week and just right AFTER the season of Cherry blossoms, the price possibly drops down because it's a kind of "off-season".
Especially during the season of Cherry blossoms, sooooooooooooooooo many, toooooooooooo many, crazy amount of people from all kind of places including the people like you visit Kyoto to enjoy it.
But sometimes, the hotel offers some discounted price for the vacant room to welcome and expecting more people to stay.
That's the answer for your first question, hope it explained enough for you.
For your 2nd question.
As I mentioned above, this season is very difficult to book a hotel even for Japanese.
Especially on weekends, it's happening whole year.
Kyoto is, as you might already know enough, very famous place, and not so big city like Tokyo.
Hotels and Temples or Shrines are placed within approx 80km.
And most of places are mountains, it's very different from other big cities like Tokyo, Osaka.
So I think if you check the booking status in May or June, you'll see enough vacancy.
According to the sightseeing association of Kyoto, they have more than 10 million foreign tourists during March to April. ( AND of course, plus Japanese tourists AND local people)
For 3rd, I think no one have the answer for that.
But one thing I maybe able to say is, it might always depends on the culture of its own, the system of its own, the season of its own countries.
I'm not sure how many countries you have been traveled, but here in Japan, the system works as you see.
If it's too expensive or looks insane, or you can't book any room that you can satisfy in Kyoto, you still have choice to stay in Osaka in stead. THOUGH, the things of surcharges or the other things you concern will be still the same.
As I mentioned, I think you should better to stay Osaka, give up staying (hotel) Kyoto.
Kyoto is special place compares to the any of other places in Japan.
And it has special culture, OWN RULES and MANNERS we all HAVE TO respect. ( And most of the people do.)
Osaka is completely different from Kyoto, so it MUST be much much much comfortable to stay for you, they will listen to any complains from you, and also you can travel by train from Osaka to Kyoto and Osaka to Kobe with short time trip.
Hope this can be your help...