Alhumdulillah, I own both the cars you have narrowed down your options to and I have have been driving both of them inter- city/intra city, have taken them to farthest areas of Punjab, where road conditions are extreme and pathetic.
Based on my personal experience and factors you have selected for your decision making process, I would suggest you to go for Altis MT.
Short delivery time , better resale (if not stolen), smooth, comfortable, durable body and suspension, have excellent acceleration (even better then 9th Gen - may be its because of 6-speed dual vvti transmission or i am using mobil1 high grade synthetic oil, don't know the reason but feels like it's slightly better than civic) and ready to take the beating on rough roads.
Two major downsides of Altis MT are its braking at high speeds and being highly prone to thefts and snatching , which you can counter or minimize by installing good quality tires and getting the ride insured.
Fuel Mileage of Altis MT= 12 Kmpl with AC within City and 15kmpl on highway.
On the other hand, Civic is also a very good car indeed, offers absolute driving pleasure (way better than Altis), peace of mind in terms of safety/security, better handling at high speeds, excellent braking, slightly expensive, delivery time is more (ranging from 2-3 months, you might get MT variant sooner than prosmatec), excellent mean of transportation for urban dwellers, can be taken to remote areas occasionally but would definitely require strict regimen of maintenance to keep the ride fit if regular trips are to be made on rough roads, otherwise definitely will start aging faster than you might even think.
Fuel Mileage = 13 kmpl with AC and 15-17 kmpl on highway depending on your driving style.
Now ultimate choice is yours both cars are good and best available options in this range.
I completely endorse your viewpoint on JDM cars Cheers!