I can only suppose that when Go Ahead and Rotala bought the Manchester and Bolton depots from First, it was in the knowledge that franchising was a very definite aspiration for TfGM and Andy Burnham. These purchases would provide a ready-made footprint/base from which to tender for routes etc.
Instead, the proposed scheme is that they could lose their purchases overnight and only receive the rock bottom price for the property. Rotala is seeking a full judicial review whilst Go Ahead initially held the same view but has now changed its position so that they don't lose everything overnight and that there's a phased transition to a world more akin to London.
Although as you correctly say, it makes clear in both the article you published and in the more detailed minutes of the GMCA which I read earlier, that such a process would not be lawful.
They could make a direct award, say, to Arriva to cover some Wigan routes if Stagecoach got the hump and pulled out of Wigan altogether. It would be justified because (in my hypothetical example) Arriva already do some routes in that area from their St Helens depot, and it would be an emergency situation to make sure there was no loss of coverage.
They could also, probably, buy a bus company outright that wanted to leave the area and make a direct award to their own in-house bus company. If the Building Buses Better document comes to fruition, it talks about allowing the public sector to create their own bus companies from scratch (again). It would be iffy from an EU law point of view as "State Aid", but of course post-Brexit, that isn't going to be the big issue it once was.
But entering into a partnership with Go Ahead as an interim (which would have the effect of freezing anybody else out), and then making a direct award to the incumbent would be against competition rules, as it would just favour one private company over all the others for no good reason.
The depots issue is a weird one. Yet another example I think of the TfGM biting off more than they can chew, without realising it (as the Strategic Rail Authority and then the DfT did with many a rail franchise over the years). They say they will buy any bus depot at "fair market value" from any operator who wants to sell. What's a "fair value"? What I'd pay for a bus depot in a deregulated Manchester where I'd be one of the biggest operators is nothing like the price I'd pay for a depot I potentially can't actually use and which would probably be too big anyway for the size of the franchises they are proposing. And presumably they plan to lease them to any operators who win the contracts. What if the operator doesn't want or need it? What if it needs upgrading?
I imagine before long they'll have some empty depots sitting there until they decide to knock them down and build houses on them (which possibility also feeds into the question of what is a "fair value").
As I understand it, in London, depots and garages are owned by the operators not TfL.
Also noteworthy from the minutes of the meeting I read is that the proposed franchising plan routes have been fixed. They definitely won't be cross-boundary as the route list is shown in an annexe and they are all stated to terminate within the GM boundary. Every adjoining local authority has raised questions about this in their reply to the consultation, Cheshire East even saying they fear a "hard border" will become established(!). Merseyside and West Yorkshire say they wish to "continue discussions". Yet nothing to suggest TfGM is taking this into account (or even cares).