The code that triggers this is:

/* The mail daemon won't have a window here, so there's nothing to set
 * as the parent */
 user_message_dialog =
		e_alert_dialog_new_for_args (NULL, error_type, m->prompt, NULL);

Can we call e_shell_get_default and then e_shell_get_active_window ?

(evolution:3739): e-utils-WARNING **: Something called e_alert_dialog_constructed() with a NULL parent window.  This is no longer legal, please fix it.

Breakpoint 1, g_logv (log_domain=0x7f06462922b3 "e-utils", 
    log_level=G_LOG_LEVEL_WARNING, 
    format=0x7f06462922e8 "Something called %s() with a NULL parent window.  This is no longer legal, please fix it.", args1=0x7fff8a8d66d0) at gmessages.c:430
430	  gboolean was_fatal = (log_level & G_LOG_FLAG_FATAL) != 0;
(gdb) bt

+ Trace 223086