I think I got a solution to fix both problems the CSV export and the report on tree structure.
First we add a forth key to the data sent to the report. It contains the indentation level for every ids (empty for list). This information can be used on the template to indent the records correctly. This prevents to compute it on the server side which may not be reliable depending on the actual root in the client and if the type of graph the tree is (if parent is a Many2One or Many2Many).
Second on ir.action we allow to specify if the action runs on the selected records or the listed record. This is similar to Issue 9090: Add export CSV route - Tryton issue tracker. For tree this means that it is the ids of all the rows which has a parent expanded.This way report that has meaning only as an all, can set this flag and always be complete (of course there are always the case of newly created node between the client read and the report generation but I think it can be understood).
Third the CSV export that are using “Listed Record” and based on a tree, we do not use the domain (which limit only to roots) but use the rows which has a parent expanded. And when formatting the lines, we add spaces to the first column following the level.