How do STEM professors become so hyper-efficient with their research? When I compare myself to my advisor, I don’t compare our level of expertise, as I don’t think that’s so meaningful; he’s obviously years ahead of me in the field, and so any time I talk about research with him, I accept that I know less than him and am prepared to feel ignorant / make mistakes / ask silly questions.

But I do compare myself to him regarding things such as efficiency, organization, motivation, curiosity ... some other things perhaps.
And I would say it is the efficiency that stands out the most – and where he completely leaves me in the dust.

Does this mean that the writing is on the wall, and that I should drop out of the race for academia now? Is it more of an innate skill that is so significant that it separates the best researchers from the rest? Or, is that extremely high level of efficiency something that is learned throughout many years of training?
Efficiency tends to rise with demand - the more demand for a resource exceeds supply, the more efficient with it you quickly learn to be. Time in the lab/office tends to follow a similar process. When you have 10 hours to write that abstract, it often takes 10 hours. When it's gotta get done in the next 45 minutes because that's the only time you have, you just write it in 45 minutes and be done with it. 

The other main issue is experience - having done this thing before - completely changes how long it takes to get something done. When you are doing something the first few times, everything is new and requires a lot of cognitive load. Nothing is automatic yet - everything is not only deliberate, but you may need to take time thinking out all the options, then going through each of a dozen possibilities trying to explore what you should try next, then wondering what you will do if that doesn't work out quite right, are you really sure that's going to work, etc. Hours (or days, or weeks, or months) of wondering and exploring can be cut down into minutes of doing. But you kind of need learn how to do it in the first place to move on to that point.

It's valuable to look up to highly effective, proficient, efficient people and try to learn from them, but there is the constant danger of discouragement if you compare where they are now - after possibly a decade or more of experience, hundreds of papers, and who knows how many collaborators and mentors they've learned from in this time - to where you are now, comparatively just starting off. And when they were just starting out, they were not so efficient as they are now (don't believe all the legends that tend to grow with time on their own, either).

I don't know how efficient you can become, and the funny thing about human growth and development is you don't really know either. No one really knows the future, or the extent of any individual's potential. It's up to you to decide if you want to find out how efficient you can become, if you can improve your organization skills, if you can cultivate greater creativity - then you can give it you all in finding out what you can accomplish, as a sort of experiment, or you can decide if you'd really rather do something else instead. But you haven't indicated anything that signifies you are doomed from the start, so long as you are willing to accept that it takes much time and sustained effort to achieve such growth in anything that you choose to do.