The preparing progress should be related to `tolerant-size-ratio`

## Enhancement Task
Now, we don't use `tolerant-size-ratio` to calculate the threshold of preparing progress so that in some cases, we will find the progress indicator isn't changed for a long time since it is blocked by the `tolerant-size-ratio` setting. Also, the previous issue mentioned that `tolerant-size-ratio` isn't suitable for some cases, like https://github.com/tikv/pd/issues/3880, https://github.com/tikv/pd/issues/3950. We need to reconsider this part once we reimplement the `tolerant-size-ratio`.