There is no excuses for doing this, or for SE to not dealing with it.

This is also very unfair towards DD's, cause for us it takes ages to find a group using DF, and if I was to withdraw, I would have to wait longer than an actual dungeon run -_-

Just add a percentage based Tome system. If you play through the whole dungeon, you get the same amount of tomes from every boss as you do right now, but if you enter a group in progress you gain tomes based on the amount of the dungeon that is left.

Instead of getting 50 Phil and 30 Myth for only doing the last boss in WP, you would get like 35 Phil and 10 Myth tomes. If you do second and last boss you would get 65 Phil and 20 Myth.... Just an example, but this way you wouldn't really gain anything from joining a group in progress. At the same time though, it wouldn't be bad to enter a group in progress.