I did this on the one day tour from Bali - I was booked on the 7am Garuda flight and with the time difference due to land at 730 am - and then depart at 730pm to return to Bali.

Due to a technical issue - did not arrive in Jog until midday, the tour guide was most apologetic - no time to visit Batik factory, market or Sultans Palace.

I only wanted to go to Borobodur.

So we drove to Borobodur - did the tour - was not at all rushed.

Then drove back went to Prambanan (which is near the airport) and even had time for a meal before being dropped back at the airport,

A long day but worth it to see Borobodur - Prambanan was interesting and worth a visit but it did not have the impact of Borobodur.

I would certainly do anything you can to organise a visit