Take this with a grain of salt as I have administered WIAT-II but it's been a few years, and I have not seen WIAT-III (there may be differences I'm not aware of). My experience with WIAT was not with gifted students either, so I don't have direct experience with interpreting scores. That said, a couple of things immediately occur to me as I read your post.
The way that the reading comprehension section is structured on the WIAT, students are given certain passages based on their current grade level. To use the computer scoring, the administrator has to administer only those passages. For a highly gifted reader, I think that there would be a ceiling effect that impacts the way in which percentiles look. The student also doesn't see the question in writing, as it is presented orally.
Pseudoword is as it sounds....made up words. It looks at a students understanding of phonics. Some students are great readers but struggle with this activity because they keep trying to make what they see into real words, or because they don't rely much on phonics to approach new words in reading. This might be a student who accumulates many new words as part of reading vocabulary, but mispronounces them when they say them out loud. This would impact the word reading score as well. It doesn't impact silent reading comprehension because they are able to infer meaning (and to attach meaning to that word from then on) even if they are unaware that they don't actually know how to pronounce it.
Math fluency: this is timed. Student works through as many problems as possible in a limited amount of time, no skips allowed. You mentioned slow processing in WISC and SBS, so I wouldn't a high score here. The more relevant score is the problem solving score which measures general content and is not timed.
Essay composition is scored subjectively and score reflects grammatical and punctuation errors, as well as spelling errors (and unless they've come up with a better prompt in version III, the prompt is bo-ring.
Oral expression is also somewhat subjective. One task is fluency (name as many.....in one minute as you can).
Personally, I don't see the connection between WIAT and science and social studies curriculum. If you have a child who chooses to read college textbooks in these subjects and who demonstrates comprehension of those textbooks, that is surely more relevant. Maybe an accommodation or agreement that he will type new vocabulary into an online dictionary as homework (so that he can hear the pronunciation of the word) could address any concerns about word reading/pseudoword.
