Well, I'm not sure about costs, it seems expensive but hard to know exactly what they are pricing. Also, I'm not quite getting why this 4 days is structured this way. Given the possible road routings, it seems they have you going from Borobudur to Solo by way of Yogya. If you will arrive at Yogya airport by 15:00, it seems to make more sense to rearrange this tour:

DAY 1: Arrive Yogya (Adisuscipto-Solo Airport), car pickup directly to Borobudur and drop at Manohara Hotel. Evening in Borobudur village. If you get into Yogya earlier...say around 13:00, you'd have time to get on the monument in the late afternoon also for a different view/feeling.

DAY 2: Borobudur for sunrise. Breakfast, then car pickup for nearby Mendut Temple (won't take long) and Kaliurang village for Merapi viewing. Back to Yogya for check-in to hotel, lunch. Afternoon sightseeing which frankly, you can do on your own. What's of interest is fairly concentrated and can be seen on foot, or with a becak (like a cyclo/autorickshaw/etc) ride.

DAY 3: Prambanan, just get a taxi from hotel. This only takes about 3 hours even done leisurely. More sightseeing and shopping (Yogya is one of the better places for Indonesian handicrafts but watch out for the schlocky fake "old" batiks), evening Ramayana ballet. Doable on your own.

DAY 4: Early rise and breakfast, car to Solo either with guide in tow, or get a guide for the day meet you there. I think you'll find that anything of interest in Solo will fit in that day. If you examine the Solo part of the itinerary you provided, you'll see there's not that much "meat" there.

DAY 5: Transfer to Solo airport (not Yogya) to fly out.

Hotels would be 1 night at Borobudur, 2 at Yogya, 1 at Solo. If you want to fly out of Yogya on Day 5 instead of Solo, then just make it 1 night at Borobudur and 3 at Yogya, and do Solo as a daytrip on Day 4. Solo is also easily accessible by train if the times work for you. I find it hard to believe that flight options out of Solo are better than those of Yogya.

In summary, my inclination would be to do my own hotel arrangements directly, do meals and entry fees on my own in real-time, and contract only for the private car with driver services for JOG-Borobudur, Borobudur-Yogya via Merapi, and Yogya-Solo-Yogya as a daytrip. If you want an English-speaking guide for the major sites (Borobudur, Prambanan, Sultan's Palace), it's really better/cheaper just to get one of the official ones at each location.

I don't have on-point comparison information for you, but in Feb 2010 for 4 days in Yogya and Borobudur (extra Yogya day but no Solo), I spent USD 65 for entry fees and on-site guiding (including the sunrise Borobudur tour) and transportation. Double it for two people = $130. Substituting in private car/driver where I used public transport and taxis instead, add another $100, then multiply by guess factor 1.30 to allow for inflation and dollar devaluation, and I calculate about USD 300 for two people excluding hotel and food. I didn't use an overall tour guide and I didn't use a guide at Prambanan. I didn't do the evening Ramayana Ballet but saw an afternoon performance instead. You might have a few extra entry fees at Solo but order of magnitude would be small.

Maybe this can be another data set you can use to calculate out whether components are better or package is better. Assuming $300 for 4 nights of hotels (should be able to get some discounts), $120 for food for two (could be cheaper), $300 per my calcs for entries/transport, $50 for misc, and you get $770. Which sounds better than 491 x 2 = $982. I think the car-only quote and car + guide quote are also high, goodly profit built in there.