I re-measured, starting at 100mm and still got the same measurement. Whew.
So, here's my dilemma (apologies for the pedantry but this feels like a "cross roads" moment that I'm going to royally stuff up!).
The left picture is with the bridge in position (using the pre-drilled holes) which gives me my scale length. The second picture shows what I think I will need to route out.
I'm just triple checking but I think I just need to use the existing pre-drilled holes for the bridge and just route out the mm or so (I think this is the way I am heading and means that the front of the bridge lines up much better with the scratch plate). I'm going to use a sanding drum and take it very slowly.
The other option (ie making sure that the pickup is happy first and then fit the bridge relative to that) worries me because I'll have to set the bridge another 1-2mm back and I don't think I'll have enough play in the saddles (ie need longer threads) and have to fill and re-drill the bridge screw holes.
I'm pretty sure that I've answered my own question now but a "You got this, Johnny. I agree with the first option" would be appreciated
Please forgive me - I hope to be a little more adventurous/less needy as I go along.