Per-card toggles
In a Rookie Box each finished card shows a Cracked Ice toggle. Switch it on for the cards you want and leave the others off; the box total shows the upgrade as its own line. The same is true in a MEGA box, at the MEGA rate.
Why a Bulk Box is different
A Bulk Box is a single design printed as a run of 25, 50, or 100. The finish is applied to the run, so it is either on for every copy or off for every copy: $14.99 for 25, $22.99 for 50, $29.99 for 100. If you want a few holographic copies and the rest standard, put the holographic copies in a Rookie Box.
The cap makes full boxes cheap
Because the Rookie Box charge stops at $14.99, upgrading five cards ($14.95) costs about the same as upgrading all eighteen ($14.99). If you are going to make more than five holographic, you may as well make the whole box.