All of the unix timestamps are in GMT. I just checked it again, and I am pretty sure. If you have a series of steps that indicate otherwise, please share them with us.
API 2.0 no longer has the server time field because it isn't necessary for syncing and was actually leading people down a path that was causing more sync problems that otherwise. You do not need to know the server time to sync. If you are concerned about how to generate the value for modafter, you can allow us to generate it for you via the account/get.php call which gives you the "lastedit_task" timestamp. All you need to do is cache this and you'll have a record of the last time you synced. You could also use the largest of the modified timestamps returned from the previous tasks/get.php call that you ran.