🚀 go-pugleaf

    Is it kosher for applications to modify the .Xdefaults file ?

In general, I would say no; users tend to organize the contents
of this file in fairly ad-hoc ways and would likely object if
you changed the organization.  Preserving the organization is
probably an intractable problem.

    If not, is there an accepted mechanism for users to modify their defaults
    by some kind of nice, user-friendly window in the application,

In the Xt case, the "application-specific user resource file" 
(the one located by XAPPLRESDIR in R3 and XUSERFILESEARCHPATH in R4)
was intended for exactly this purpose.  It's a separate file which
(normally) lives somewhere in the user's home directory and the
intent was that applications store the results of a "customize
this application" session there.  Applications should still
preserve anything they find in this file that they don't have
reason to override, but it's not expected to be as free-form as
.Xdefaults.

    It seems confusing to have geometry specifications in both the .Xdefaults and an
    .applrc file

Yes, it would be, but the contents of .Xdefaults are entirely the
user's resonsibility.  A friendly application might warn the user
that there is extra stuff in .Xdefaults when it goes to write its
application-specific resource file, but I would still leave it to
the user to figure out what s/he really means.

    Other question.

Can't help you much there, but using a selection to allow clients
to rendez-vous and then open a separate channel between themselves
is exactly the direction we've been advising for high-bandwidth needs
-- at least until the more generic network computing services become
more universally available.