Yes, "all else being equal" is correct. Let me rephrase the sentence...
"If all women had the same work hours and workload, STEM workers would be earning 33% more."
This means that, women who work in STEM jobs earn more NOT because their jobs are different. they have similar (equal) jobs to other women BUT they still earn more. Because if you want to compare two things accurately, you need to put them on equal grounds first, you know?
So, "all else being equal" means "if everything OTHER THAN their pay is considered equal"
At least, this is how I understood it. hope this answers your question.