OCJD
I can tell you what my experience has been, since it sounds like our kids might have some similarities in that he isn't "knocking it out of the park" across the board. We had our DS8, also in 3rd grade, take the WISC-IV to see if he qualified for DYS. He scored a 142, but his GAI was also not high enough for DYS so our situations are different, but I have some thoughts on Achievement Testing.

DS8 also took the WIAT test, which I know is different than the Woodcock Johnson, but it is an achievement test nonetheless. I think a student who has been allowed to work at their ability level will do much better on an achievement test than kids who are bright but who are learning at the "age specific" rate of teaching. There is no acceleration at our current school so DS wasn't exposed to much above his grade level but was able to figure out some of the more difficult questions, like fractions. My son did not do well on this test at all, however. When we had our follow up meeting with the tester, she showed us some of our son's work and he made mistakes, seemingly on purpose, on things I know he knows. For example, when subtracting double digit numbers he didn't do any borrowing. He had been doing this for a LONG time and he was (re)learning it in 2nd grade while he was sitting for the test. In the writing section, the test would give a word and the child was to write a sentence using that word. Well, on one question the word was "until", and DS7 (at the time), writes, "I can't wait until this test is over." (HA!, he is his father's son!)

My point is, it depends upon the temperament of the child and what they have been exposed to. I would not discount the portfolio option if your little guy sounds like our lovable DS.