We've all been there with replacement parts that don't quite align with each other and need work, easy or otherwise to get them to match up. I'm currently putting together a parts bass using a body from a Fender Road Worn Jazz and a new, WD Products direct replacement neck. The neck pretty much dropped right in (after a bit of rough-sanding the pocket) but when I went to fit the Gotoh ferrules they weren't 'push-fit'. I had an authentic vintage Fender set looked out as well and they didn't fit, either!
The specs of the WD neck ferrule holes are 17.4mm whilst the Gotoh ferrules are 17.6mm but I reckon the latter are out by a bit more than 0.2mm. I've had this across every aftermarket neck and tuners, with Wilkinson sometimes being the worst offenders. To that end, I bought a couple of hand reaming tools a few years ago and it looks like they're going to get used again.