But, many drivers appear to call tty_flip_buffer_push() from an atomic
context. If that is done with tty->low_latency==1 it turns into a call
to flush_to_ldisc(), which then calls disc->ops->receive_buf(), which
must not be called from an atomic context.

It's covered under "So don't do that then".

Is the low_latency flag being forced to 0 somewhere behind the scenes
when tty_flip_buffer_push() is being called from an atomic context?

No. The driver authors are assumed to have a modicum of competence and if
they don't usually a shower of lock debug messages enlightens
appropriately.

Alan