http_timeout value will be stored in frappe-bench/sites/common_site_config.json on execution of command bench config http_timeout 6000
then the bench setup nginx configures it to the given timeout
by default if there is no value it takes 120
SSD will require less timeout,
HDD will require more timeout,
using bench console will not timeout,
Other related things :
Is the filesystem type ext4? (refer following)