So the old timer code for mining had a minimum timer of 4.5s before bonuses are applied, with an absolute minimum of 2.5s. With the change I made it so your base timer is calculated based on your skill/ql and bonuses, then that is added onto the base 2.5s time (so there is no 2s buffer that bonuses take out of). What you're seeing here is the diminishing returns you get at these very high skill and ql levels.
With 99.999 skill and a 95ql pickaxe (no enchants or anything), your timer would be about 3.06s, and swapping that for a 97ql pickaxe the timer would go down to 2.83s (due to how ql comes into play when getting skill for these checks). Removing the base 2.5s timer we get 0.56s and 0.33s to work with on the bonuses. 100 WoA or BotD would make the biggest difference here, cutting those down to 0.28s and 0.165s, but other bonuses like runes and rarity only do about 10% each, which isn't much when you're getting this low.
We could change this back to the minimum no-bonus timer is 4.5s to give the bonuses more to work with, but I think it is a more fair system like this - where bonuses matter more for those that haven't maxed out their skill or item QLs.
Edit: Some more numbers now that I'm looking at it - previously if the average of your skill + pickaxe ql was over 93.3, you were wasting your time as it would not lower the timer any further. Now over that mark you'll still see timer reductions without having to use any bonuses.