Discounting the V-22 OpsreyOsprey and the other tiltrotors, the drawbacks are:
- Wasted cabin space
- L-duct inlet(s) needed to guide the air in
- With that potential problems with getting the air in as the air prefers fewer turns
- A reduction gearbox is still needed
- Gearbox still needed for the tail rotor
- Harder maintenance access as it will be buried into the fuselage
- If the exhaust is channeled downwards: potential tarmac melting, fuselage weakening, and handling issues in low hover
- If channeled upwards, well, that's where the rotor iswhere the rotor is
- Otherwise, extra heat ducting needed, i.e., added complexity and weight and expensive materials
- Any fire or uncontained failure will cause grave danger.
Below is the best illustration I could find, and it gives you an idea about the previous points: