Edit: Considering the upgrades from the engineers are very powerful indeed - doubling or tripling stats in extreme cases, one could argue that players who continue to "play their own way" are effectively locked out of 60% of the ship progression possible in Elite. You may view that as a fair consequence of their chosen play style, I believe it is an unfortunate limitation to our ability to play as we want to play.
While I share that view - the perversion of the "blaze your own trail" tagline - doing so for the sake of upgrades
is only a temporary thing, ie go off and spend a bit of time to satisfy the requirements, come back and never have to do it again.
I had a great little excursion with another CMDR last night; I wanted some nanobreakers but couldn't find them anywhere and the item drops were frustrating me, so he offered to provide them in return for me sourcing some commodities and doing an exchange. He surprised me with some really good RP, and I had to go and buy a T7 and do some trading to get what he wanted; I'm normally a combat pilot, so that was a total departure into something I generally don't find fun at all.
Turns out it was a nice break from my usual playing style.
My point? A brief departure into other professions isn't a bad thing,
when there's a definite goal with 100% chance of being satisfied once you've completed it. In this case, the 5000Ly requirement is solid, and there's a definite reward at the end of it - and if you take an advanced scanner with you, you can boost your exploration rank to expose more missions too.
Not the worst thing in the world, especially when considered against the frustration of the randomness of the rest of the Engineer interactions.