Are these circuits equivalent? (Arduino on breadboard)
Long story short, no.

Think of the circuit diagrams you drew as ideal cases. In reality, there are stray capacitances, inductances and resistances surrounding all of those pins and traces. That's why there are two physically separated caps, and removing one actually matters. The placement of the caps matters, and you should be following the recommendations.

If it were an ideal circuit, then your two diagrams may be electrically equivalent, but there's no such thing as an ideal circuit.