I'm not sure if our situation is exactly the same but it has enough similarities that I'd say it qualifies

! My dd13 subject accelerated by one year in language arts in 3rd grade (the only year they were willing to do this) and then skipped 5th grade as a whole later. She is now a 9th grader, so accelerated one year in everything, and is further subject accelerating in science by taking both the 9th and 10th grade science courses this year.
I'd say that it is wonderful that they are willing to start subject acceleration this early. I don't imagine that he'll miss out on much so early in the process. For all subjects but math we never saw any gaps with skipping a year or more. For math, both of my girls have subject accelerated one year so not as much as your little guy, but they weren't offered this until much later in the game. They both missed the 5th grade year of math to move into 6th grade math (dd13 due to the grade skip, dd11 due to subject acceleration). There were a few math concepts that they hadn't learned at that juncture but they were fairly quickly filled in.
The fact that your school doesn't have a gifted program might turn out to be a good thing if they continue to be so open to making alternate arrangements for your ds. What we found in schools with gifted programs was that a lot of the kids were tracked into the GT classes and they were somewhat of a status symbol. They generally did not meet the needs of highly gifted kids and the schools were less accommodating regarding alternatives b/c they felt that they had a gifted program so it should be enough for all gifted kids regardless of the variety btwn those kids.