real quick, give me your opinion on what I should put down:
both my birth name and gender?
put down my birth name and perfered gender?
and some applications have the option to not put down any gender

if its optional to put gender id say dont put one down. even if you have too, id maybe try to get by by 'forgetting' to mark either box.  and since its a legal thing, id think youd have to put your legal name down, but if theres a way you can put 'perferred name' or a nickname, then put down your male name/perferred name.

this is the complicated part with things, which is why i made sure i get my name and gender marker changed before getting my new job, to avoid confusion and awkwardness.

Unless otherwise specified, job applications require your legally correct information.  They want your legal name, legal gender, legal address, etc.  If you give them legally incorrect information, it'll disqualify you from employment.  And they will discover your legal name and gender at some point during the hiring process.  It's necessary for tax purposes.  So give them the gender that's on your driver's license.

I would either try not to put one, or if you have to, put your "legal" gender.

If you are in the US, they cannot legally ask you for your gender. They can, and now often do, have a section that is supposedly for statistical tracking where they ask for gender, race and military experience. These are always optional.

As has already been stated, if information is required on an application, then your legal status is required. When I answer the optional gender questions, I use female - because that is how I identify and what I am (just not legally, yet).