If I’m reading your question correctly, the answer really depends on what you choose for the characteristics of your engines and generators; their efficiency, waste products, energy requirements, operating lifetimes, and so on.
If your conversion process is fast, clean, efficient, and truly fuel-agnostic, then it doesn’t matter what you use - you won’t need much of it anyway. Depending on the service life of your generators, you might even buy one with a lifetime of fuel already built in. At 100% efficiency, 1kg of mass converts to 9e18 J using the usual formula. That’s more than a 2 gigaton nuclear bomb, which is a problem if you decide to crash at full speed, but that’s another discussion. Thermodynamics will most likely limit how much of that you can use for propulsion, but its still a ridiculous amount. The current annual world energy consumption could be produced by converting just 61kg of mass if you assume perfectly efficiency (1).
You mentioned a fueling infrastructure - tankers, stations and fuel deliveries. That implies that while people could use anything and everything as fuel, at least some people don’t. Somebody goes to the trouble and expense of operating a fleet of tankers and filling stations in a world where fuel is free, so we need a reason for that. The tankers also imply that this fuel comes from a limited number of locations and has to be transported rather than being manufactured everywhere it’s used - again, we need a reason.
Consider a real-world example as a point of reference: A conventional 3000MW fission reactor converts pretty close to 1 kg of mass to energy every year (2). To accomplish this, it consumes 25 tons of enriched uranium fuel and produces 1 kg less than that in waste. That’s only 0.004% efficiency give or take, but it is genuine mass-energy conversion. The energy takes the form of heat, which we use to generate electricity. We could theoretically convert that same mass and generate that same heat using lots of other, cheaper processes, but we use uranium fission because it produces energy at a good rate, is a controllable reaction, it isn’t too short lived, isn’t too rare, and so on. 435
These same considerations could apply to your fuel. What characteristics could make a good fuel worth transporting if you can have other fuel for free?
1) Performance: some materials could convert more efficiently than others. If it takes several tons of cheap junk to produce the same power as one gram of good stuff, it will be well worth it for anybody who needs better acceleration, longer flight times, or bigger payload capacities. 2) Safety: some materials might be riskier than others - maybe you can control the reaction rate better with some things than others, or maybe using the wrong thing risks damaging your generator or worse. Sure, you can save a few credits by connecting your generator to the san, but they used cheaper fuel rods at Chernobyl too and see where that got them. 3) Convenience: some materials could produce nastier waste products than others, making waste storage, handling and disposal a real show stopper. Perhaps pure rocket fuel converts cleanly and completely, while random junk will convert just fine and get you where you’re going, but it spews out loads of hard radiation in the process and leaves you with a residue of poisonous radioactive acid potion smeared all over the engine room. 4) Legality: Depending on your setting, smart devices and materials could be a consideration. Your generator might refuse to accept any other fuel than the genuine original manufacturer’s special blend. A government could even issue fuel that carried an encrypted signature so that your generator would only burn it while on a registered flight path. That might serve as a solution to the Kzinti Lesson(3) or the aforementioned 2 gigaton bomb problem as well.
On the other hand, maybe those tankers and fuel stations don’t really dispense fuel at all, and are called that for historic reasons. If those electric engines you mentioned are regular reaction engines you’ll need to take on reaction mass from time to time. That's what the tankers and stations are all about. For fuel, you just siphon off a few grams of reaction mass to feed your generator since you have tons of it with you anyway.
(1) https://www.bp.com/en/global/corporate/energy-economics/statistical-review-of-world-energy.html
(2) https://www.nuclear-power.com/nuclear-power-plant/nuclear-fuel/fuel-consumption-of-conventional-reactor/
(3) http://www.projectrho.com/public_html/rocket/spacegunexotic.php#id--Propulsion_Systems 435