> this really makes the engineer's end of the bargain sound like janitorial work
I don't think you should interpret it that way. Another take would be that its like collaborating with a domain expert outside your specialization.
Important is that your potential impact as an engineer can grow as you become more knowledgeable in the relevant bio. Most of the scientists I've worked with were happy to teach background (and some were just exceptional, fun times if you also found the field interesting as I did!). Obviously some allowance must be made for differences in culture from org to org, and that likely accounts to some of the disappointed voices - but I'm not convinced this is endemic to the field as opposed to organization specific. Just like with an opportunity with any particular company, do your research.
Incidentally, working on a well defined engineering+optimization problem, if you are lucky enough to bump into one, is just candy for lots of engineering types. Ok quick & simple one: a scientist I worked with was doing some analysis that involved intersecting piles of genomic intervals with each other, which was taking many hours for a single run - super painful to tweak and re-execute. Our team showed them how to use interval-trees and made these available integrated in our internal tools, and the problem transformed into ~10 min execution runs. See, a wee a bit of comp-sci where suddenly you're the domain expert. And appropriately appreciated!