NPN Transistor Behavior with Base Voltage higher than Collector
With 0 on Q1's base, Q1 will saturate to probably within 100mV of the 5V rail i.e about 4.9V on the collector. If it were an NPN emitter follower and you applied 5V to the base, the emitter would be at 4.3V - maybe that's where you are having a minor bit of confusion?

With Q2's base sitting at 4.9V and its collector being at (say) 3.3V you'll have a heavily forward biased base-collector diode (un-natural operations) and may indeed damage Q2 due to excessive current flow.

Iif you had (say) a 10k resistor in series with Q2's base this would protect the device and you would see a voltage of nearly 3.3V on the emitter because Q2 would be saturated-on.