So, I thought about this on my 25'; and, arrived at this conclusion. On previous boats I've owned, I sometimes would set two rodes but only during conditions which warranted two anchors. This occured for me only under two conditions: (1) when I had planned to stay out several days in known areas where it would make sense to carry the second anchor; and, (2) during long stays (generally lasting longer than several days) in unknown waters - both to accomodate conditions which could turn adverse. Since my last couple boats were walk-around center consoles, I simply brought the extra anchor and rode along in a box (sometimes) or simply tossed it up in the bow area.
On the 25', I intend to about the same. Rather than carrying the second rode w/ me all of the time, I'm still opting for carrying it only when I believe it's warranted. For me, it justifies why I don't carry a second anchor+rode all of the time, and allows me more inside storage space.
I think if I were to accomodate a full-time second anchor and rode, I would probably opt for your intended storage area; or, I would consider building a box for the cockpit and securing it to the port-side of the cockpit area with some method of yet undetermined but cleverly crafted means.
I'm currently carrying 400' of rode (x2 200' rode lines) in my anchor locker and on the 25', I still have room for another 400' - which I am very thankful for. In fact, during the next couple of months I'm going to secure a set of cleats to hold the anchor locker lazerette door open while navigating inside the anchor locker. That bloody door is painful and bothersome to maintain in the open state when you have to attend the rode - ugh!
Actually, I just thought of something - could be a real loser thought, but - have you considered simply extending your anchor locker and rebuilding it to accomodate a larger amount of rode and two anchors? That might be a good option.