One of the smaller details which matters to some, & not so much to others, is the hook keeper on the rod. While it's not a huge decision, it can be something to consider. When it comes to fly rods, you have a couple of choices in the style of hook keepers.
The main function of the keeper, obviously is that it hold the hook well (strung up on the leader & line). So, it must be the right size for the size of hook you'll be using. Also, the hook keeper should be light weight, as you don't want to add extra, unnecessary weight to the rod. In addition, you want the hook keeper to look like it belongs on the rod, so the metal color, etc should match the line guides.
The first style of hook keeper is probably the most common seen on rods today. These are sometimes referred to as "u-shaped" keepers.
The next style of hook keeper is what we call the "strap & ring" style. These are fancier than the u-shaped keepers. Here a strap holds down a loose ring that holds the hook. These have a traditional, classic look. Most of them are made from Nickle-Silver which means they will patina over time like other NiS hardware on the rod. While they are what's most seen on bamboo rods, they can add a nice touch to graphite or glass fly rods too.
So while it might not be the first thing that comes to your mind when choosing the options on your custom rod, you certainly do have some options available. All the little details like this add up to make your custom fly rod truly unique & special.