Yeah that should work - I messed up mine on the first pass, but it was easy enough to plug and re-drill. Annoying for you as its come form the factory like that. Are you going with a scratch plate on this? I'd also check that fit and how the bridge sits in it before re-drilling.
Build 1 - Shoegazer MK1 JMA-1
Build 2 - The Relliecaster TL-1
Build 3 - The Black Cherry SG AG-1
Build 4 - The Sonicaster TL-1ish
Build 5 - The Steampunker Bass YB-4
Build 6 - The Howling Gowing ST-1
"What I lack in talent I make up for with enthusiasm"
I've developed a habit now, over the previous 3 builds to get it PLAYING first. Then surface finish. Then fiddle with it to make it feel and sound just right. The plan is if I can get a neck pickup fitting in a tidy way then no scratch plate. Later today I'll investigate possibilities of a Jazzmaster pickup.