In P&N, that kind of multi-requirement guessing game is handled by having a cheaper component available when you've only got one of the two requirements. It is also quite clear as to what you need, most of the time.
You want "armored engines"? get propulsion and get armor.
Biocrystal armor? Crystalline and organic tech.
Battlemoons take ship and base construction, but there are no empty levels, you'll still get a better ship/base hull no matter what.
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The problem is, SE4 still lets you research Generic Ship Construction 3/4, you just don't get anything until you research Construction I. So to the user, it can appear that Battleships and Dreadnaughts require Construction I.. then they try that next game and nothing happens until they research Generic Ship Construction II/III.
If there is absolutely nothing to gain from researching "Generic ship con" level 3 until "construction" level 1 is researched, then I'd suggest:
- Make Generic Ship Con stop at level 2
- have Construction open up a new tech area, "Large Generic Ship Construction"
If there is nothing to tie levels 1&2 to 3&4, you hight as well split them up and save confusion.
In the other hand, you could try placing a dummy hull size "Prototype Battleship" which is almost useless as a ship, and whose description indicates that you require advances in construction techniques in order to actually build one.
Something like Triple Maintenance would be good to use as part of the hull, which would simulate the prototype nature. None of the replacement parts can be mass produced yet.