That's not abnormal, I haven't made one of these kits though. Its a Tuneomatic style bridge on these isn't it? The issue with doing any sanding on the heel or in the pocket is that you may alter the break angle of the neck. It's doable, but a lot of care must be taken. It may be a better idea to remove material from the neck heel rather than the pocket as it'll be easier to take it down evenly.

See what others have to say before you do anything, but I suspect it will be fine to leave as is.