This is incredible feedback! I appreciate you taking the time to write the post and provide the feedback about the bugs! Some of these I am aware of and will patch in the next version.
I am glad you were able to figure out that there are reasons for upgrading the earlier layers even when you get deeper into the game. The synergy of the chain reaction, pierce, hardness, and health all play a role in how far you can instakill multiple layers. I don't think many people will notice this right away.
For the issue with max rocks being 10, there will be no cap, but right now there's no way to expand the total quarry size past 10. That's a planned prestige upgrade. For now I'll leave it because it won't be an issue once I add prestige.
I will add a scrollbar to all scrollable areas.
Thank you so much for your feedback! I am glad you have enjoyed the game in its current state. A lot of players have said it is too slow and the upgrades aren't impactful enough. I have a major rebalance update in the works for upgrades, drones, and bombs.