Yeah, wait for the Wilkinson to drill holes as they are a bit different to the kit ones. You've picked the common issue with these kits. You can assemble as is and it works fine, but you can also absolutely enlarge the bridge cavity and move the whole thing forward to close up that gap without any dramas, there is enough adjustment on the screws to take it up.
You can see me going through the same process in this first TL build I did
https://www.buildyourownguitar.com.a...ead.php?t=8005
Oh also, I wouldn't be using the center fret markers as any kind of guide. The High and Low E string is the best way to make sure everything is running true.