To answer your questions:
1. Pickups: The red triangles are enemies. The round glowing objects (green/blue/gold) are pickups — hovering over them collects them. They are all good!
2. Boss & "3 Levels": The game is actually a roguelite with no end. You die, keep your Skill Points (SP), upgrade your tree, and try again. Level 3 is just the first boss. You get stronger every run!
3. Resetting: To keep your progress, always click "Next Run" after dying, not "New Game" (New Game wipes your run).
4. Mobile UI: You are 100% right. The game is designed for PC right now, and the forced rotation makes the UI too small on phones. I am actively working on a dedicated mobile update (v3.8.0) to fix the layout and touch controls.