New staff should be on a standardised contract (including Sunday in the working week!) but there may not be a case for ever going through the extreme pain of harmonising everyone, particularly not people who only have maybe 10 or fewer years to retirement, though an offer could certainly be made to get people to voluntarily switch if they'd prefer.
I suspect what they really mean by saying they are going to harmonise pay is that they aren’t going to try and harmonise Ts and Cs.
It’s the plethora of differences that have been negotiated by individual TOCs over the years that will be the issue: In general terms the TOCs that pay the most have more stringent Ts and Cs. So how do you go about imposing a “standard” set of Ts and Cs across the industry?
The idea of new people being on different (worse) Ts and Cs isn’t really one the unions will swallow. Even if you ignore the union objections it would cause a great deal of complication in terms of rostering; having different links of Sundays inside and Sundays outside can just about work, but if drivers also have different movements off spare, different annual leave entitlements etc. it becomes a great deal more complex. It would also take many years to filter through if the changes only apply to new joiners.
In short, I can see why they aren’t going to go there: it’s too complicated, and with very little scope for meaningful savings.
This sort of thing is less of a problem in office based roles where (broadly) everyone just expects to work standard-ish office hours Monday to Friday, and there’s much less variation. Even then you can get issues with differing pension and annual leave entitlements etc. when different businesses merge.