I fully agree with the OP, there is a lack of logic and "realism" on the whole engineer concept. Frankly speaking, the only thing that I like about engineers is the modded modules. The resulting variation of characteristics can make ship building a game of its own. Too bad I'm hindered by the periodical material gather (I'm not the guy who will tell you "you will gather the materials by playing the game how you like"). Periodically, I grind using all the tricks and shortcuts in the game (crashed ships, missions, barnacles, brain trees, installations, you name it) and renew my stash of materials. The actual game is, for me, between those gatherings. Imagine living on an island without electricity and, in order to play some game on your computer, you have to pedal to recharge the batteries: that's material gathering for me.
Not to mention the cringe-worthy blueprints or recipes... Someone at Frontier probably just discovered Mendeleev's table and said: "Problem solved!". The game could've been way more interesting with an actual logic construction: rare, I mean rare materials to be discovered on planes or asteroids, parts to be bought, ordered or fabricated and the whole thing going somewhere to your secret base where you modify your ships... Just a thought.