Both while and whereas are perfectly fine in academic writing. The important thing to remember, is that while has another meaning relating to time. It says that one action takes place at the same time as another. If you aren't careful, it can sometimes be ambiguous as to which meaning is intended:
- While Obama introduced Medicaid, Bush started two wars.
Here the sentence could mislead the reader for a second, because it sounds as if Obama and Bush were doing these things at the same time. If there is any chance of being misunderstood or making your sentence a bit more difficult to understand, don't use while or whilst.
This is a matter of style guides
Journals and other publishers may have their own in-house guidelines when it comes to usage and grammar. Many follow the top style guides: APA, CMS, and MLA. Social science and economics related journals may very well follow something totally different than the hard sciences.
What you have linked in the comments, is a guide specific to your graduate school. Universities may or may not follow one of the top three style guides. In your case it does; your graduate school follows the APA style guide (scroll to the end of that website and you will see the source).
Some universities even make up their own guides, which are usually very generic and less comprehensive than the top three. Note that university guides may also be inconsistent sometimes (i.e., they take certain things from APA and certain things from CMS and then put them together). And this is why you will rarely find scholarly publications that have exactly the same usage, grammar, and overall style as your university guide (unless your school follows the same style strictly).
Now to address your specific concern, here's what Chicago Manual of Style says (17th ed.) about the verb tense (which is different than what your school follows):
Usage and Grammar
Q. Chicago recommends using the present tense when discussing the actions of characters in literature. But I often face questions about verb tense when discussing the actions of authors themselves, particularly in academic writing. Is it correct to say, “Blomley (2004) argues that property claims can be used toward ends that are both oppressive and emancipatory,” or should I instead render the verb in the past tense? Would the answer change if Blomley had written his book in, say, 1867?
A. Regardless of how long ago the author wrote, the “historic present” is commonly used in just this type of context. If you want to emphasize the past, however—perhaps to contrast it with the present—the past tense works well. Absolute consistency needn’t be a goal in a long manuscript, but don’t mix tenses near each other. Source
Another one:
Citation, Documentation of Sources
Q. Dear Chicago, what verb tense do you recommend for the literature review section of a scholarly article? APA insists on the past tense, arguing that any work included in a literature review was obviously published in the past. People writing about English literature, on the other hand, discuss works in the present tense because readers always experience the book in the present. I’m editing a Canadian public policy journal, and the author uses the present tense to discuss works published ten or fifteen years ago. Should I change these tenses to the present perfect? The journal has no in-house rule on this.
A. Since the use of the present tense in literature reviews is widely accepted, and since any decision about where to cut off “past” from “present” literature would have to be arbitrary, using the present tense for everything is a fine option. You shouldn’t worry about using it if a journal doesn’t express a preference. Source
And another one:
Usage and Grammar
Q. When writing about an author’s work, do you write in the past or present tense? Example: The author argues (argued) that it was the correct choice. Please help. Thanks.
A. Different kinds of writing have different conventions. In academic writing, it’s not wrong to use the past tense when quoting written works, but it’s conventional to use the “historical present,” even when the author is dead (Heraclitus says, “No one steps into the same river twice”) ... Source
It is possible that the top-class published journals that you are referring to did not follow the APA style guide, which is the source material for your university's guideline.
APA
...
Describing a method or procedure
Simple past tense
- The participants were interviewed ...
Present perfect tense
- Other researchers have followed a similar procedure.
Source: Use of verb tenses in APA, Chicago and MLA styles
Best Answer
For academic writing, I would check to see if there is an applicable style guide - your college or university may have their own guide.
Generally speaking though, commas are more formal than dashes or parentheses. Parenthetical information is often defined as useful or interesting but also disposable and could be omitted. A written piece with lots of brackets doesn't look as professional because it gives the appearance of lots of superfluous afterthoughts. Parenthetical information between commas is generally seen as being more relevant. Bracketed information is often abbreviated, while information in parenthetical commas should maintain the grammar of the sentence and be 'readable'.