Well, I think what happens here is that the new SJE code alters the subquery (by removing ref_2) and that change is not propagated into the parent level. So in the parent level, when we look at the subquery's original targetlist (which remains unchanged) against 'subroot' (which has been changed accordingly), we'd have problem.
AFAICS there are two solutions being discussed:
1) We propagate the change to the subquery into the parent level by ensuring that root->parse references the same Query structure during the whole subquery_planner().
2) In the parent level, we look at the changed subquery instead of the original rte->subquery. IOW, we look at subroot->parse->targetList instead of subquery->targetList.
Personally I prefer the second solution because it seems more natural to look at 'subroot->parse' together with 'subroot' in estimate_num_groups and it does not introduce new constraint to subquery_planner().
FWIW, here is a simplified query that can reproduce this error.
explain (costs off) select ref_1.c17 from t2 ref_1 left join t2 ref_2 on ref_1.vkey = ref_2.vkey where ref_2.vkey is not null except all select c17 from t2 ref_3; ERROR: no relation entry for relid 1
