Assuming we can use methane, ethanol, water, ammonia, or whatever, as unprocessed fuel, do we adjust the percentages, considering hydrogen density, lower?
Best answer is ... "it's complicated" ... because each feedstock source has different binding energies for the hydrogen in the molecules. Some, like ammonia, will actually be able to increase the amount of hydrogen contained within a unit of volume because of how the hydrogen atoms are bound within those molecules while they're not organized as H
2 molecules. A tank of ammonia contains about 1.5x the number of hydrogen "components" per unit of volume compared to an identical tank of H
2 (for example). Problem is, the process of making/generating ammonia is endothermic, so you have to put energy IN before you can get ammonia OUT for transportation/use of the energy stored in the ammonia.
Gets back to the point I made earlier ... every time you "convert" energy from one form to another, you aren't going to be doing so at 100% efficiency (because: Three Laws of Thermodynamics).
When you've (literally) got nothing better ... you use what you have, no matter how (net) inefficient the energy supply chain is.
Reciprocating piston steam power is wastefully inefficient compared to turbine steam power ... but if all you can manufacture are pistons, then you use what you've got (which in Traveller terms is a tech level limitation). You use pistons to convert thermal energy into linear mechanical energy, then convert again into angular rotary energy ... and so on and so forth ... until finally reaching the end of the sequence resulting in useful work (of whatever variety is needed).
As far as starship fuel purification plant processing goes ... the rules are substantially agnostic on the question of unrefined fuel sources. This then leaves it as a question for Referees to adjudicate whether or not the fuel purification plant installed on YOUR starship can "strip" hydrogen from a wide variety of liquid and gaseous sources of "raw" chemistry found in nature.
My own assumption would be similar to that of LBB5.80 in that streamlined craft can access liquid water (lakes, oceans) under atmosphere, so the fuel scoops in streamlined craft include the capacity for liquid "unrefined fuel" intake (regardless of chemistry, albeit within limits). Partially streamlined craft, which are limited to fuel scooping from the outer atmospheric layers of gas giants, would be able to deal with gaseous/heated into plasma by orbital velocity aerobraking maneuvers fuel scooping, but wouldn't be able to handle liquid state intakes.
So the best answer to your question is ... IT DEPENDS ... on a lot of variables, including environment the unrefined fuel is being gathered from and the "power plant" system (chemical or fusion) it needs to be routed through to generate the desired levels of energy needed for applications. Chemistry ... is complicated ... especially if you don't have "the right kind of equipment" to do it with.
