1/ engine noise is a function of the rpm and gear ratios. the 1.6 is a more powerful engine and thus registers lower rpm than a 1.3 at similar speed. Also the 4th gear ratio of this transmission is a slightly GREATER overdrive than the fifth of the manual resulting in higher speeds at lower rpm.
2/ the above details fit here too.
5/ Gli a/t has an older engine (VVTI against Dual VVTI), a Thailand Toyota transmission - the 1.6 has a Japanese aisin warner transmission- no alloys and no navigation. The choice is clear for some and not so clear for others. you'll have to figure it out yourself.
all the best!