Understanding the use of English tenses in biological journal articles
I regard this is more of a question for SE English Language and Usage under the tag “technical”, and will vote to move it there. However, as the answer relates to reading papers in molecular biology, I provide an answer here.
Linguistic interpretation without context
The tense used in the phrase “X remains poorly understood”, taken in isolation, suggests that this is the situation now. Hence, it is the situation at the end of the study.
However…
Interpretation in context
This is the Introduction section of the paper. In the Introduction to papers reporting experimental biological research, it is usual (and helpful to the reader) to explain the background to the study and why it was undertaken. In this case to explain that the incomplete understanding of the subject justified further studies such as the one to be described.
This is made clear at the end  of the Introduction, where one often indicates in a sentence what the work to be described adds to knowledge: “Our results show that flagellum originated very early, before the diversification of contemporary bacterial phyla…”.
So the minimal implication is that as a result of the work described “X is now better understood”. And that is clearly the case here.
This is borne out by the final paragraph of the Results section in which the authors emphasize the contribution to knowledge that their work has made. You don’t get published in PNAS by saying that you have left the field still in the dark!
Why not use a different tense and say that you the problem has been solved?
An alternative would have been to write:
“Before this work was undertaken X was poorly understood”
The reason for not doing this could either be “scientific modesty” (also known as don’t antagonize the referees by appearing arrogant) or acknowledgement that, despite the significance of the work presented, there are still aspects of the problem that are not understood.