Quite possible, if they can accept shared running between trains and metrolink Wigan to Hindley Junction. But GMTE where also looking at Metrolink to Bolton as a possibility.
I totally agree with you on this point, but they are being put in charge of transport for the regions, and will want to be seen to have some impact whilst at the same time they won't want the other city region having control over transport under their remit. The only way they won't get bogged down in bureaucratic nonsense is to have clear splits where their jurisdiction ends.
Have you heard of Rail North? If you haven't, I'd seriously suggest that you look up their web-site.
Could you also suggest a source for the suggestion that Metrolink to Bolton, if it ever happens, would be over the L&Y route via Farnworth?
You are trying to create problems that don't exist in the interest of unnecessary angst at the implications of pointless solutions.