I'm no timetabling genius nor light rail expert, but I would say the following.
The MCUK service turns at Velopark for an operational reason, indeed the advertised service of the MCUK shuttle is currently only to Cornbrook - and it always has been. Thus people are 'counting their eggs' by thinking the present service to Piccadilly will last forever.
It's thought by some that the most suitable candidate for through-running to Ashton when it eventually gets its 6 minute service is the Eccles service.
The MediaCityUK service can't really run through the East Manchester line at all because it needs to arrive 6 mins out from the Eccles services - so it cannot possibly arrive 6 mins out from the Bury services as well can it? Eventually, two trams would arrive at exactly the same time.
Indeed, even running empty through to Velopark to turn back, it holds up the Droylsden services and would do so even more if it were loading and unloading at the first four stops. It would also serve the wrong platform at Velopark! This assumes that there are actually some passengers to from these stations, and there are not exactly a lot of them...
Lastly, I'm fairly sure the infrastructure work has been completed on time for the double ended turnback at Cornbrook? Well, there was never going to be a west-facing bay platform here and the fact that the turnback can't be used is not TfGM's fault!