I think the 709 is called something else nowdays, but I think it does go in your record.

Assuming you pass, it should not hurt as much as a violation or checkride failure...if you had really done something wrong, they would have violated you.

There are two kinds...formally it's intended to be a verification of pilot skills in a case where there is a possibility of doubt. If you pass, you should be fine.

Informally, the 709 can be punitive if you PO your FSDO. There would have to be some previous history for this to be the case, personality conflict, or bad reputation on the field. You would know in advance if this was the case, and of course you would not pass a punitive 709.