Two co-first author publications vs. one second author + one first author publication Hypothetically, which of these authorship scenarios would look better to the eyes of a potential employer in the academic world of biology/bioengineering from the perspective of author A:

Work 1: author B*, author A*, author C - moderate potential for impact

Work 2: author A*, author B*, author C - moderate to high potential for impact

*these authors contributed equally

OR

Work 1: author B, author A, author C - moderate potential for impact

Work 2: author A, author B, author C - moderate to high potential for impact

My colleague and I have a theorist/experimentalist relationship with a work that has since fractured into two separate works. The second work is more theory focused while the first is more experiment focused. We believe the second work has a more broad ranged application and has potential to be heavily cited.

Pragmatically, author A is close to finishing his PhD and, besides these two works, he has one first author paper.
First, I want to make it clear that I am not in your field, and do not know what relevant people's attitudes to co-first authorship are. In addition, answers and comments to What does first authorship really mean? suggest that they may actually be different between biology and biomedical engineering, so that might be something to pay attention to as well.

The main point I'd like to make is that the nature of the papers can (and should!) matter - I would at least that to happen in my own field. Say if the more experiment-focused paper has minimal theory/modeling, and the theory-focused paper only uses previously published experimental data... Well, if the contributions look incommensurate (and remember that the journal might require author contributions to be clearly stated), people are going to see right through that co-first authorship - and that can reflect poorly on both authors. Even if the journal does not require a description of individual contributions, A would likely be asked about their individual contribution in a postdoc interview situation, for example.

Hence I would always suggest picking the natural/ethical author order over a strategic one. It's also generally better to get a paper out this week than having it delayed a month over an authorship order debate or prolonged strategic analysis... Co-first authorship should be considered if there are clear arguments for it on the level of an individual paper.

Now, overall I actually expect the two scenarios to have fairly similar outcomes (again with the caveat that I'm not from your field) - especially since I suspect C to be the advisor, who'd presumably write a fair recommendation letter either way. If pushed, I would say that the second scenario could hold a slight strategic advantage for author A, since A could appear to have a higher degree of intellectual leadership in the higher-impact paper. If it is more theory-focused anyway that may well be the case.