Because Honda's auto transmission, despite being 5 speed, has more load on that 100HP engine than Toyota's auto transmission.
Varient for Varient, current gen Honda Civic weighs 10-15 KG more than equally equipped current gen corolla internationally.
Pakistani civic is 1275KG so even Grande wouldn't exceed that.
Corolla internationally starts at 1240KG (much more equipped + 1.6 liter engine minimum)
I'm sure Pakistani Gli is less than that but since we don't have official numbers. Assume that it is indeed 1240KG.
the difference with City is 85KG that's the slightly above average weight for a guy in Pakistan I'm sure it doesn't make much difference in fuel economy.
What makes the difference is Honda's 5 speed transmission in city has much more parasitic load.
GLI auto is just 84HP so it is ought to be sluggish but City Auto is just as sluggish
which means that honda's auto transmission is robbing 10-15 HP off,. Making it work extra hard.
I've been a passenger in an auto city that heated up (transmission heatup) while going up hill to highland resort, it's fuel economy was miserable as well.
City 1.5 on the other hand has better fuel economy in automatic transmission as it's manual varient's gears ratios are short for a 1.5-1.6 liter engine.