We've got users working in the same project located in Europe (CET), UK (GMT), and US (EST), server hosted in on GMT. Issues require an action before a deadline is reached (DateTime custom field).
We have a JQL that uses the endOfDay function to see what is due today (deadline < endofday())
I've had a look at the source code & it does seem to respect the user's timezone but what I'm not certain about is when it's run as a Subscription to a group of users.
From memory, I think the subscription runs the search for every user in turn so that it only returns the data appropriate to the permission levels. I'm guessing this picks up the users timezeone as well.
So... 3 users, in 3 time zones, same subscription, same permissions could get 3 different sets of results based on their time zones.
Does that sound right?