Caveat: been a while since I had anything to do with Puma 2, so things may have moved on!
The Makilas have been flying around with analogue cockpits in the 332 for thirty years
Yes, but not necessarily the RAF Puma cockpit (330E, effectively an RAF specific version of the 330B, which gives you some idea of its vintage!). To fit the Makilas and leave the same cockpit in would have required EC/MoD/QinetiQ etc to start from scratch with the design and certification process, as that work has, tmk, never been done. EC had already done the certification work (to JAR-29) on the Makila mod when they sold it to its previous customers, so QinetiQ need only to work on the delta between the Def Stans and JAR-29, rather than the whole shooting match (that was the case early on in the programme, if that's no longer the case I stand corrected), which saves money. If the Makilas could have been fitted to the Puma with the old cockpit still in, and it was cheaper doing it that way than doing it with the glass cockpit, that is what would have happened.
I would have thought that introducing the glass cockpit at the same time was for flying and operational reasons with their obvious benefits
It would be nice to think so, but no. It happily does bring those benefits, as well as the performance increase that the Makilas bring, and the extra fuel from having the 5th tank back in. But that was not the driver for this programme.
The whole thing has only been done in order to get anticipators on the Puma so it can stag on for another 10 years. Anticipators requires Makilas, the Makila mod brings the glass cockpit. The glass cockpit is only there because it comes with the Makilas.
The only reason it was done this way is because it is the cheapest way.