Dear @Omaer
First of all keep in mind that corolla never offered an automatic in 1300 and 1600cc in 2009/2010 ...... Automatic was only offered in top of the line variant aka Altis Cruisetronic SR in 1800cc.... The simplest of the Altis was called altis cruisetronic without sunroof.
Now coming to the rest of your queries
1. Yes there is a difference of 1-2 km/l between manual and automatic transmission. Manual is always better in fuel consumption.
2. Milage of automatic altis is maximum 8-9km/l withincity with ac on.
3. Do not buy a car exceeding mileage of 85000km but you need real expertise to evaluate it otherwise most of the cars are meter tempered. On the safer side make sure you are buying car from first owner himself.
4. Yes corolla performs very well on CNG.
5. Yes corolla is very reliable.
6. No , already mentioned in the start.
7. Market price of a clean altis 2009 -2010 is between 11-13 lakh .... ( depending on condition and sunroof option )
My recommendations
First of all you have to make your mind that you need a Petrol car Or you want a car to be run on CNG.
Secondly you have to decide between manual or automatic.
Thirdly you have to decide between toyota or honda.
If you don't have CNG availability issue only then you go for CNG compatible car otherwise search for only petrol efficient car.
In case if CNG is a must and only Toyota automatic is the priority then i will recommend you to go for a previous shape SE saloon automatic(2002-2005) or Altis automatic (2005-2007)with CNG they are the most rough and tough CNG compatible cars .... 2009 /2010 altis is not that cng supportive car because engine valves needs replacement within 100,000 km and it has poor resale as well.
On the other hand if CNG is must and honda can also be considered then try to find a clean city 1300 manual or auto 2009/10 ..... It is most fuel efficient in terms of petrol as well as with CNG.