As a practical matter, this is probably correct even though that isn't how the rule is worded. The guidelines for determining level do specify that both level of degree & experience required as well as supervision of others are considerations in making the determination. See pages 6 and 7 of this document: http://www.foreignlaborcert.doleta.gov/pdf/NPWHC_Guidance_Revised_11_2009.pdf for an explanation; note that Level 3 mentions that they should consider "key words" that define supervisory responsibilities.
Prevailing wage encompasses base salary alone - you are correct. The value of Benefits isn't included, and bonus can't be counted because it isn't a guaranteed component of compensation (a bonus is something that isn't promised in any specific amount, even if there is a normal range).
Speak with an attorney for further guidance on your case.