Is it? It's not a refurb, it's swapping the seats, rejigging the reservation screens and adding a (presumably modular) buffet. Would give a stock of FISA LEANs as spares, too.
FWIW I think ordering two types was silly. They could always have peddled First Class tickets on StanEx for say a £5-10 upgrade, and just left the buffet closed.
I think in the original thread about 745 construction and introduction there were some "issues" with designing and fitting the buffet, so there might be structural mods to do. I'm not really sure. Remember also there are quite a lot of table bays in the 745/0s (I don't think there are any in a 745/1), and with USB and 3 pin power at every seat pair there's significant wiring mods required too.
At a time when railway costs are undoubtedly under scrutiny, I can't imagine going to the DfT/treasury with the begging bowl to fund a refurb for 18 month old trains is going to go down too well.
Completely agree with your second point, it really doesn't make any sense. It may have been driven by a desire to provide extra luggage space for the Stanex units which then required a denser seating layout to compensate - perhaps No. of seats was a franchise committment.
But from a real world POV, it's a little bit silly and clearly it has proved extremely difficult in practice to make sure the correct sub-fleet is used on the correct service.