For sure, by all means!
It is entirely up to you how to use any free space you may have below your cabin sole
I'm certainly no expert, but...
For the sake of stability... I would suggest you use the space for something heavy such as fuel / water tankage or batteries
If you decide to add another tank athwart the keel
then it would be a good idea to add baffels in order to reduce Free Surface Effect.
If the space in question is fore & aft on the centerline then I'd put batteries
I reckon it primarily depends on what your future intentions with your boat.
If you plan to meander along with the trade
winds then water may be best.
If you're crossing the equator then fuel may be better.
If you're just gonna hang around Hawaii
then I'd fill the space with da kine.
It's up to you.
It sounds like you're in a very good position to create a custom interior
layout just the way you'd like it... which is enviable. Just make sure the berth and settees are at least as long as you are tall.
But - to answer your question... I've never really wished that my fuel tanks were bigger
I departed the Ala Wei bound for Saipan in 1995 with 40 gallons of fuel and arrived 31 days & 3500 miles later with 36 gallons... only because my refrigerator
was broken. The most fuel I ever
carried in the 25,000 miles since then was about 100 gallons (aboard a 37 ft boat powered with a 30 hp Yanmar) when we set out from the Canaries
across to the Caribbean
. And this time the fridge was
working... and we still arrived with plenty fuel.
I'll probably do it differently next time... but I'm really not sure.
But that's just me.