The variation to the staircase was due to head height restrictions on the bottom few treads. By removing one stair, they were able to fix that up. Unfortunately they aren't able to send us colour schematics of the updated staircase, and it is quite a big upgrade so it would have been nice to see.
The alteration to WIR1 of the Master Bedroom doesn't appear to be too much of a big deal. They have had to extend the void that backs on to WIR1 by 35mm, and the amount of space we're losing to our shelf width is 15mm.
We've signed and submitted the variations and updated plans. Let's hope the end result is ok, especially on the stairs!