which seems to be really hard for people to wrap their heads around:
I don't think this to be the case, just people has different views than you and see many problems in your house rules. If you ask for thoughts, you msut assume you'll get many criticisms from people that thinks differently to you.
I agree with many people that the staterooms are too small, at least for commercial passages (military people have to accept quite worst conditions than people who pay for a stateroom). Current world ships are not a valid analogy, as (as you said yourself, BTW) on them you can always go to the deck for fresh air and to ease the claustrophobia. Sea chips cruiser staterooms use to be even smaller, I agree, but you use to spend little time on them, sleeping time asside. On a starship, OTOH, you probably spend quite more time on them, and the rest on the halls, that would aslo be quite smaller in your system.
Another major problem I see is for subcrafts hangars. With Traveller rules, a 10 dt subcraft would need about 210 kl hangar, and if configurations are similar, you can expect to be able use them for several different desings of 10 dt crafts. In your rules, the volume (and so hangar needs) of a 10 dton subcraft may vary depending on its armor (I guess armored ships to be more dense), its mission (I guess a refuelling shuttle will be less dense when empty, but more when full than a passengers one, and many other factors, so the hangars must be configurated for a specific ship, and things like the modular cutter are fully ruled out.
As hinted in the above point, the mass of a ship can vary from empty to full...
Fuel can also be re-defined as hydrogen compounds (...). Specifically, water or ammonia.
This has been discussed many times. Water (to talk about the easiest to calculate) mass is about 1/9 hydrogen and the rest oxygen. So you can hold a ton of hydrogen in 9 kl, being, as you say, more efficient (when volume is the limiting factor) than Lhyd, but not so when the limiting factor is mass (as your rules suggest), as to have a sinlge ton of fuel you'd need 9 tons of mass.
A J2 ship needs 20% of its tonnage as hydrogen fuel to jump. If your limiting factor is mass, and to have a ton of hydrogen you need 9 tons of water, you need to carry 180% of your tonnage as fuel (if dtons are volume, OTOH, carrying the fuel as water would reduce the needs to just under 13% to keep those 20 tons of hydrogen per 100 dtons of ship)...
This aside, how long do you need to extract the hydrogen from it? I frankly have no idea, but I guess jumps would take quite a longer time...
Another problem with your rules, this time metagaming, is that it makes all current ship plans useless, so taking many gaming resources out of the players' and referees' hands...
Your line of thought may be valid, I won't deny it, but would give a very different paradigm than the one most Traveller players and referees are used to.