Thanks Fernando, I am testing with the current development branch and I confirm this issue has been fixed and Matlab and Octave behave identically. I am not sure when this got fixed but this is great news!
Thank you to whoever fixed this and this report can now be closed.

¯\(°_o)/¯ with the foo class defined in comment #1, subsref is indeed called in Matlab for f.a(end)=1;

>> f = foo ();
>> f.a = 1;
subsasgn
>> f.a(1)
subsref
ans =
     1
>> f.a(end)
subsref
subsref
ans =
     1
>> f.a(end)=1
subsref
subsasgn
f =
       foo object: 1-by-1

If I define an "end" method like this:

function ind = end(obj, k, n)
  disp ("end");
  ind = 1;
end

the above doesn't change and the new method is only called for:

>> f(end)
end
subsref
ans =
  struct with fields:
    a: 1

Define the following class with subsref and subsasgn methods

%%% @foo/foo.m
function obj = foo ()
  obj = struct ("store", []);
  obj = class(obj, 'foo');
end

%%% @foo/subsref.m
function val = subsref (obj, S)
  disp ("subsref");
  val = builtin ("subsref", obj.store, S);
end

%%% @foo/subsasgn.m
function obj = subsasgn (obj, S, val)
  disp ("subsasgn");
  obj.store = builtin ("subsasgn", obj.store, S, val);
end

In Matlab:

>> f = foo ();
>> f.a.b = 1;
subsasgn
>> f.a.b
subsref
ans =
     1

In Octave 5.1 or 6.0:

octave:1> f = foo ();
octave:2> f.a.b = 1;
subsref
error: null_matrix cannot be indexed with .
error: called from
    subsref at line 3 column 7
octave:2> f.a = 1;
subsasgn

I don't think that subsref should be called when evaluating "f.a.b = 1;"