1) Yes slightly better ground clearance.
2) Japanese alto comes in AGS and CVT transmission. CVT is very smooth. Since no gear change. AGS is similar to PKDM, AGS in Japanese alto comes in the 2 or 3 basic variants and in alto works sports edition. The cars with dual transmission are AGS not trip tronic.
3) pretty much yes. Just that the local alto has metal fenders, Japanese alto has Fibre glass fenders.
4) Not much reasons. Peace of mind of being new is the only reason. Comfort wise a Japanese CVT would be more fun to drive in my opinion.
AGS is excellent in gears above 2
First 2 gears make the drive really uncomfortable if you are driving in small stop and go traffic