Ok I've tried with the tip instead of 1.4.3 and it somehow works better, but
still some bug.

New Test Case:
mkdir mercurial mercurial2
cd mercurial
hg init /tmp/nested_absolute
echo test > /tmp/nested_absolute/foo
hg -R /tmp/nested_absolute add
hg -R /tmp/nested_absolute ci -mtest
hg init nested_relative
echo test2 > nested_relative/foo2
hg -R nested_relative add
hg -R nested_relative ci -mtest2
hg init main
echo nested_relative = ../nested_relative > main/.hgsub
echo nested_absolute = /tmp/nested_absolute >> main/.hgsub
hg -R main add
hg -R main ci -m "add subrepos"
cd ..
hg clone mercurial/main mercurial2/main
cat mercurial2/main/nested_absolute/.hg/hgrc
mercurial2/main/nested_relative/.hg/hgrc

I got as result:
[paths]
default = /tmp/nested_absolute
[paths]
default = ../nested_relative

The relative subrepos defaut path is not correctly set (should be
../mercurial/nested_relative or /tmp/mercurial/nested_relative). And somehow
I don't think that this is logical to reference the absolute URL in the
originial repo instead of referencing the working copy.

I will make another patch (on the tip this time !) and send it to the devel
mailing-list