[lld][LayoutPass] This commit fixes a problem in the
Layoutpass by ordering atoms if they appear in the override
list first and then looking at the way of ordering atoms in
the default way.

The fix also fixes issues with the sizes of the sections,
that appear in the output properly too.

The commit also adds a testcase(orderatoms-by-override.test)
to test it and fixes all the other relevant testcases.