I have had no urge to modify any of my Yamahas at all. Pickups are fantastic, the other hardware is great, the basses themselves are well made and the fit and finish is outstanding.
Mine haven’t had fret sprout but you can definitely feel the frets along the edge. There’s nothing to file or round off, I think it’s just how Yamaha cuts frets - you notice them. I think Josh even mentioned it in his TRBX304 review.
If I had kept my Warwick Rockbasses, I would have replaced the EQ’s with 3-band. I dislike 2-band EQs a lot. And put in active/passive switches while I was in there.