I am not an expert but will tell you about my experiences so that you can analyze.
I have always been a manual tranny fan. However, I had a Prosmatec in 2005 which was converted to CNG in 2006. Only after a couple of months the kit was removed and sold. Reason being the poor performance of car and the jerks that were affecting the gearbox. That Prosmatec got sold and a manual one was bought. I do miss automatic transmission when I am stuck in traffic however. But then, you have to let go something in order to get something...
Now lets come to Reborn. I have a manual on CNG as well as a Prosmatec on CNG. The manual is simply too good on CNG. The car mostly runs on Petrol but when it is converted to CNG, you don't feel too much of a difference. If you don't get involved in races, then even the pick is just perfect for you, else, it goes above 150 easily on CNG. For places like Pakistan, it is more than enough. Regarding the mileage, on long runs it'll give you around 150 kms per cylinder i.e. for around 600 rupees or less, it will give you around or above 150 kms easily and that too if you drive it at higher RPMs. Within city it gives minimum 100 kms per cylinder if you drive it very aggressively. If you drive it with care and at lower RPMs, then the mileage can cross 125 kms per cylinder. Therefore it is extremely economical and is way better mileage than on petrol. There is a difference if you compare the mileage on Petrol and CNG which might not be too much in the early years but the margin will increase with the passage of time.
For example, if I go to Sialkot on CNG in my Civic, I have to get it refilled just once after crossing Jhelum. The CNG then takes me to Sialkot and enough remains in the cylinder that I can drive in city for a couple of days more... One sided trip costs around 900 to 1000 rupees. On petrol, it takes atleast half tank to take me to Sialkot.
Now lets talk about Prosmatec (Reborn). The car came to Sialkot on petrol this time because the performace on CNG wasn't satisfactory. I have driven it hardly five times on CNG and am not satisfied at all. You might not feel much difference in the speed, drive etc. but the shifting response is effected and even the shifting is not smooth. But again, the plus point is the mileage. But the kind of people I have around me would prefer their pleasure of driving on Petrol rather than mileage it is giving on CNG. The Prosmatec transmissions are sensitive and expensive so one should not mess with it.
Regarding resale; if it is a clean piece, then people wont leave it until and unless they are looking specifically for a Prosmatec. Some people can't drive manual cars due to reasons. So they would only go for an automatic transmission car. Rest, you still have a huge market for "nonProsmatec" lovers... Apart from that, it would be an Oriel. Demand would have been and issue if the choice was to make between an Oriel and a hardtop one.
Verdict: If you want CNG in anyway, go for Manual. The only difference it'll make while selling is that it will go a bit cheaper than Prosmatec because you got it a bit cheaper in the first place...