Why not make XP boost gain to tools based on penalty of mining speed per Y. Make that player will gain same XP per min on Y-0 and Y-100 (so reduction of speed based on Y will not reduce XP gain, with no reason, like I think).
Or even give some boost to tool XP gain the more near you to Y-0 (so it will be like 2x per min on Y-0).

This 2 min to harvest obsidian, it must give like 200x XP...

Nice idea, but i dont know how to make this possible.
Tool Progression mod give no handles for changing xp gaining.

I don't know how to change that.
If you know the way - feel free to comment and open this issue again.