It's so that the automatic assignment system does not place a high-ranked commander for your special ships.
But it will take those same R4s and R5s and assign them to ships I don't want them commanding. Now that I've lowered the ships I do want them commanding to R3 requirements, I hope the better commanders of higher rank get assigned (because those ships are larger and more heavily armed). If not, I just have to manually reassign officers after the big batch promotions.
I've read that page several times now and I see no statement that R4 is not checked and that it only checks for R3.
From the "Leaders" wiki page, it's hidden so you have to click "show":
Auto-assignment takes place for ships, fighter squadrons and ground units without commanders, using the following sequence (required bonus in parentheses): Survey ships with R3 requirement (Survey Bonus)
Armed ships with R3 requirement (Crew Training)
Unarmed ships with R3 requirement (Crew Training)
HQ assignments (Ground Unit Training)
Survey ships with R2 requirement (Survey Bonus)
Armed ships with R2 requirement (Crew Training)
Fighter Squadrons (Crew Training)
Unarmed ships with R2 requirement (Crew Training)
Survey ships with R1 requirement (Survey Bonus)
Jump Gate Construction Ships (Factory Production)
Terraformers (Terraforming)
Fuel Harvesters (Mining)
Mining Ships (Mining)
Salvage Ships (Factory Production)
Assault Divisions (Ground Combat)
Armed ships with R1 requirement (Crew Training)
Infantry, Garrison and Engineers (Ground Combat)
Unarmed ships with R1 requirement (Crew Training)
It really does say R3. The assumption that the logic would apply to higher rank grades was all on me.