You can't stipulate that funding to, say, Macclesfield should be part shared. The problem with the rail network is you can't just turn a train round at a random point - unlike a bus service where it can simply terminate at the town / village on the boundary.
The benefit of increasing services between Macc & Manchester or Warrington or Glossop and Manchester for that matter is almost entirely to the economy of Manchester. The prime traffic flows will be to Manchester and once there travellers will spend their money in Manchester, be it shopping, going to concerts, theatre or sports events.
In that context the authorities in which Macc, Warrington or Glossop lie have little or no benefit to reap from increasing the subsidies for further services.
FWIW, in London, TFL have funded outside their bounday in very specific cases, with bus and train services to Watford, and bus services to Borehamwood and Waltham Cross as examples. They recognised that the bulk of the flow will be INTO London and benefit areas of London.
Let us not compare TfL with TfGM. The only comparison is with their respective acronyms. You make mention of the train services provision and not terminating trains at county boundaries. I was of the opinion that Northern Rail as part of their franchaise agreement had control of such matters, I was not aware that TfGM had obtained TOC status.
Where does TfGM receive its funding from and what is this funding supposed to cover? It just cannot go looking outside its remit and have a philanthropic view of other areas when dealing with the monies allocated to it, It has its own budgetry planning and has to be accountable to the 10 areas that make up Greater Manchester. Cheshire East council may well plead poverty on certain matters when it suits them, but again, that is just a cynical financial ploy to say that TfGM should make up any shortfall. Let Cheshire East Council go to Central Government and plead their case for extra funding in these days when Central Government is looking for Ministerial Department financial savings.
As I said in an earlier posting, if Central Government say that TfGM were to be financial administrators for extra funding for areas outside its remit and these monies were granted, then all well and good.
If you want an anomoly to consider, look at the single rail fare from Greenfield (in TfGM area) to the next station of Marsden (in WY Metro area). Two stations, both in Metropolitan areas but with no responsibility for the connecting section, small as it is, admitted to by either party. According to your reasoning, either TfGM or WY Metro should cover the cost of this link from their budgets, but neither of them do so. Please feel free to look at the cost of a single rail journey on the National Rail Enquiries web site...you will be amazed at the price of the ticket.