There is never perfect design, for everyone's taste. Look at original MM6, how flawed is, you get fly on day 1, then head to dragons, get +20 stats asap. Then you can get expert air in few days, then fly, then town portal, is this good design for you? At least this mod has not such shortcuts.
Basically I think a good RPG design is about flexibility, and lack of any unwanted, illogical elements. The great thing is about the original MM6 is that you can play the game in any style you want. Yes, you can have the fly scroll on day 1, but you don't have to use it. No one holds a gun to your head to soft-cheat. Again, you can start the game with four knights (I did it several times) and there will be no flying and beaconing neither in the early nor in the late game. It's up to you, it is your game, you can destroy it or build it for yourself.
In this mod I find that flexibility is bleeding from a lot of wounds. I had to follow the designer's path because other options are not open. It was frustrating to get skills on expert level which I never wanted, and be forced to learn an otherwise totally useless skill on master level (diplomacy). But you are right; this is a free mod, so I won't complain about this. But stealing dozens of skill points from a character all of a sudden, it is a whole different thing. In every universe I know this is called a bug, and a serious one. And if the designer was aware about this, then the bug is in him, not in the program.
To develop a character to expert dark level 23 is my call, and nothing of the designer's business. There was a concepction behind it and the game destroyed it completely, without any reason. Looking back I would say it was a waste of skill points anyway, because the best way to kill the mosters in the late phase of the game is sword and arrows. So I would not develop a character this way again. But I want to discover this through my own learnings, not as a consequence of the designer's decision.
That's my point.