The main disadvantage with high floor/platform is the difficulty of providing platforms on street sections, as a high platform and ramps needs more space and can't really be part of the general footway as a low platform can. This isn't really an issue for tram-train in the Manchester area, as the city centre platforms are already there (although they do limit tram-trains to about 60m long). The benefit for tram-trains is that they can serve the same platforms as conventional trains if necessary, rather than having to provide a dual-height platform as at Rotherham Central, which costs money and may be difficult to do at some stations. A high floor tram train can also have a better seating layout, as the seats don't have to fit round the running gear that projects above the floor on a low-floor vehicle.
All the railway stations converted to Metrolink in Phase 3 had the platforms ripped out and replaced, so building them for high floor would have been a smidgen more expensive than for low floor, due to more concrete in the platforms and in most cases longer approach ramps. I doubt this was more than a tiny percentage of the cost of the station.