I disagree. We always suggest to our lower level legionmates to put some points in to engineers... because engineers never go out of style. But more importantly because raiding is a direct comparison between the crews of the two ships. So if you have no crew, then you won't succeed at raids. And if you don't get yellow badges from raiding, then you don't get one of the better modules in the game, protean armories. Getting protean armories becomes much more difficult the later in the game you try it, so we always recommend low level players get them while they can. Because even if it's a pain in the butt, they really are worth it.

Now, back to your question. I see no reason that doing the xecti mission chain would change the deck/engineer ratios we recommend. And they are a bit fluid to be honest as it all depends on if you're succeeding at raids. But we generally recommend a ratio of 4 rank points in decks and 1 rank point in engineers until you get all three proteans. Some players who are having difficulties with raiding may be counselled to put more points into engineers at a lower rank for that ratio to then be balanced out at higher ranks. It all just depends on what you want.