The fretboard can be levelled by scraping. I'd use a sharp craft knife/Stanley knife blade or a single-sided razorblade and just drag it between the frets on the edge. You shouldn't have to do that though.

If you've been on the forum for a while, you'll know that the headstock tuner holes are rarely perfectly aligned. Sometimes you can live with them, and sometimes people plug them and redrill them. You'd probably only have to plug two holes to get the holes relatively level to one another e.g.

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Top one down slightly, bottom one up a bit.

The new holes shouldn't be too far off centre from the old ones, so that the tuner washers will cover the work on the headstock face. The tuner bodies themselves should cover the work on the rear. Easy to check. If not, then you can always stick a piece of veneer on the headstock to patch things up.

But definitely let Pit Bull know about the issues. Posting faults here unfortunately rarely gets picked up by the PB team, so you need to let them know directly if they are to ever improve matters.