@Drasnighta With full respect for your competence and contributions as a rules guy, I don't see anything in the Armada rules as written that requires a ship to be chosen before an upgrade card is selected. You refer to what seems to be a very good mental flowchard of how one might implement rules of fleet building, but as written that is not described as a process:
Fleet Building
Each player builds a fleet by choosing ships, squadrons, and upgrade cards whose total fleet point cost does not exceed the total agreed upon by the players. The fleet point cost of each ship, squadron, and upgrade is printed in the lower-right corner of the card.
As part of building a fleet, each player must choose three objective cards, one from each category.
• The standard fleet point total is 300 points. If playing with just the core set, the recommended fleet point total is 180.
• Players may build fleets of any fleet point total as long as they both agree on the total.
• A fleet must be either Rebel-aligned or Imperial-aligned. It cannot contain any ships, squadrons, or upgrades that are aligned with the opposing faction.
• A fleet must have one flagship and cannot have more than one flagship.
• A fleet cannot spend more than one third of its fleet points, rounded up, on squadrons.
Going by the Golden Rule rule that "Effects on components such as cards sometimes contradict rules found in the Learn to Play or Rules Reference booklets. In these situations, the component’s effect takes precedence. If a card effect uses the word “cannot,” that effect is absolute." an upgrade card be worded to permit an unaligned faction ship by overriding the ship building rule above. (The cannot clause only refers to cards, not RRG rules).
My biggest concerns would be game balance implications, and preventing confusion on the game map, a rebel controlled ship would need to have very obvious markers.