The cost of the 2.5-3gallon kegs are more than it would cost you to purchase a larger co2 tank.
I am a big fan of having spares of everything. I now have 10 CO2 tanks, and 80 kegs, and a lot of other redundant hardware.
The cost to fill a 20# tank is not going to be 4x as much as it is to fill your 5# tank at most air supply stores like airgas where you swap. It may only be 5-10 more dollars for a swap of the larger tank, and the savings will be evident years down the road.
I really don't feel like you would be wasting much gas filling the headspace.
An option is to use 2-3L soda bottles and use the carbonator cap on them. Thing is, each one of those things is around 15 dollars. You can make your own using schrader valves, and there are guides online, just be careful with the materials it is made from.
Also, if you are doing experimental batches, I would recommend doing around a 2.5-3 gallon batch anyway to minimize any differences that could be magnified in the smaller batch. For me, since I do 10g batches, an experimental batch would be 5 gallons. If you have enough kegs to keg the experimental batches in them, I think that would be the easiest method with your current equipment.