I am absolutely no expert. But since my dd took the WPPSI at 3y5mo, I have read quite a bit on these boards about the WPPSI. And time and again, people will say that often test results are not as accurate on children that young.
If your gut is telling you the FSIQ is an underestimate, then I wouldn't hesitate to retest DS once he gets a few more years under his belt.
And, like you said, he's still the same amazing little guy you've always known. A number is just a number. And with testing that young, it could be far from accurate.