How can I make better use of the dead space under my bottle cages?
Good question - I've wondered the same.

I looked at the Specialized SWAT toolbox for inspiration, but it only fit certain models of frame.
https://www.specialized.com/us/en/equipment/bike-accessories/swat-technology/c/swatstorage





Another option is to mount things directly to the waterbottle cage mounts.  Here's another specialized product to do exactly that:


https://www.specialized.com/us/en/emt-cage-mount-mtb-tool-for-right-zee-cage/p/132369

Downsides of this is that it only fits their multitool and nothing else.  Also exposes the tool to a lot of dirt and muck that it wouldn't see if higher up.



I have tried a solution of using a frame mount bag right at the front of the main triangle.   Advantages are that its forward weight so helps me keep the front wheel down on a steel climb, and I can put a USB battery in here for powering my gopro on long rides.




Alright this bag was measured for another bike so its a bit saggy here.  The pump hook gets in the way, and the downtube is much smaller and a different angle from the designed bike.  Flaws - the zip is the wrong way around, and should close forward so cables can come out easier.  Velcro is all wrong for this bike.

I also use a top-tube bag for more storage when on a long ride.   That holds snacks and my phone running on another USB battery (because its annoying when strava stops recording.)