Acho que sua confusão está no uso de -l e -u para hwclock .
Note that using the --utc or --localtime options with the hwclock command does not mean you are displaying the hardware clock time in UTC or local time.
O que isto significa é que quando você executa:
hwclock -u
Você não está exibindo a hora no utc, está dizendo ao sistema para interpretar o hwclock em UTC e vice-versa com -l .
Da página do manual:
-u, --utc
--localtime
Indicates that the Hardware Clock is kept in Coordinated Universal
Time or local time, respectively. It is your choice whether to keep
your clock in UTC or local time, but nothing in the clock tells
which you've chosen. So this option is how you give that information
to hwclock. If you specify the wrong one of these options (or
specify neither and take a wrong default), both setting and querying
of the Hardware Clock will be messed up.
If you specify neither --utc nor --localtime , the default is whichever
was specified the last time hwclock was used to set the clock (i.e.
hwclock was successfully run with the --set, --systohc, or --adjust
options), as recorded in the adjtime file. If the adjtime file
doesn't exist, the default is local time.
( Fonte )