LNER passenger numbers only grew 4% in a year per ORR figures (table 1.1) and people travelled 1% shorter distance (table 2.2), although that might be bit of extra split ticketing
LNER cut number of trains run by 6% (tables 4.1 and 5.1)
So to say they have had some of the best growth seems wrong as near bottom of the growth in passenger numbers tables
But the tables show volumes and kilometers operated, not average ticket price so revenue change might not be consistent with volume
The lease costs aren't known, all we know is amount CAF receive for building them and maintaining them for few years.
We know from recent Alstom 8 year cross country maintenance contract that they are about £1000 per day per vehicle, but newer electric trains ought to be less.
The Treasury probably looked at refurbishing but calculated costs weren't good for relatively short timescale (serious life extension work at 32 years on a train with nominal life of nearer 35 years is unlikely to make economic sense).