A seems awkward (are so doing in compliance) compared to B. Are you sure it is the OA ? What is the source and can you post the full question.

I agree with Sam. It sounds awkward and generally in English doing so is preferred, not so doing.

yeah, "In doing so" and "in so doing" are used interchangeably.

The question is whether the following are different in meaning
A)if they are so doing in compliance with state laws
B)if in doing so they comply with state laws

Also on a second look at the options

Unlike the law protecting endangered animals, the fish and wildlife service's listing of endangered plants does not prohibit collectors to take listed plants from the wild if in doing so they comply with state laws

A)from taking listed plants from the wild if they are so doing in compliance with state laws
B)from taking listed plants from the wild if in doing so they comply with state laws

Do you think the reason A is the answer is That in the second option they could refer to both plants and collectors but in the first option they is less ambigous because it is clear that here "they" is the doer of the action referred to "in doing so" ????

Please mention the source. This looks really bad.

Thanks.