Chapter 5, end game awards, is going to take some thinking as Traveller doesn't grok that you didn't leave the military
Meaning benefits?
Doesn't really matter - benefits are 'the stuff that you have' - in theory you could have them whilst still being in the military; they're odds and ends you've picked up as gifts, trophies, and personal curios. They may be rolled for at the end, but that doesn't mean in background terms you don't get them until then (especially if you've been through multiple careers). High Guard works perfectly well for navy campaigns - the only trick is for survival rolls to cause mishaps but not eject you from the career, so everyone's still a starfleet officer of one rank or another come start-of-game.
The benefits system works - one roll per term means that a more senior person will have more stuff. All that needs to be considered is what sort of things are on offer.
They shouldn't be 'standard kit' - a weapon benefit shouldn't be a personal phaser pistol because anyone going dirtside will be issued one anyway.
A Mark XIII phase pistol with some sort of custom sight, that's distinctly non-starfleet issue, is a different matter, and perfectly in keeping for the man with gun combat (energy pistols)/3 - as a crack marksman he may well have done a stretch in a trials & evaluation team, and got issued a prototype.
Equally, a klingon or gorn captain might have a standard
federation phaser pistol, taken from a particularly worthy opponent/ally.
Will be interested to see the ship combat system. I'd assume (possibly wrongly) that the core mechanics won't change much (point defence, damage, etc), because (a) it ceases to be the traveller ruleset and (b) they work.
However the moment you introduce tactical FTL, obviously something needs changing, even if it's just the range bands, and (at present) there's no provision for "shields".
(The best version of shields I've seen used in game to date is High Guard's reinforced hull - it gives you a damage sink but still allows damage to leak through onto critical systems like sensors, drives and weapons.)
The other big thing is some sort of power management - it just wouldn't be right if you couldn't "divert emergency power to shields!"