I was mining quartz to repair my pickaxe with Mending and noticed that when the durability on my tool updates, it resets the mining time to mine the next quartz ore. Similar to switching tools when mining a block resets the duration to destroy it. I'm not too technical in the realms of developing but if I were to venture a guess I would say that when the mending repairs the pickaxe, it updates the pickaxe and the game code reads that as a different tool. I'm not sure if this was prevalent in previous versions but I don't remember it being a problem.