Most of the Rikudō no Jutsu abilities lost their narrative weight during the war.
1. When Madara manifested his Kanseitai Susanoo, he stated it to be his full power, despite having the Rinnegan's Rikudō no Jutsu.
2. When Madara was revived, he declared that if he were to use the Rinnegan's true powers, a sophisticated battle would take place, and Limbo Hengoku was employed right after he said this — an ability he couldn't use as an Edo Tensei.
So clearly by narrative/portrayal, Limbo & Susanoo > Rikudō no Jutsu for Madara.
Likewise, it's Amenotejikara & Susanoo > Rikudō no Jutsu for Sasuke because Amenotejikara is Sasuke's Limbo equivalent.
That's just how it is. Not only does Sasuke have a preferred move-set (likes to incorporate Chidori, Katon, Amaterasu, etc.) and the writers have a limit to how many abilities they can implement in a fight, but narratively, the Rikudō no Jutsu were clearly cast aside, with nothing more than the occasional use of Tendō and Gakidō for both Madara and Sasuke.
-----
Regardless, Isshiki can also deal with what you mentioned more easily than against Amenotejikara & Susanoo.
1. As far as we know, the 5 second cooldown likely still applies to Shinra Tensei & Banshō Ten'in, so even if Sasuke repels Isshiki's rods or repels Isshiki himself, he would have to wait 5 seconds before using either of them again.
And what would happen is even if Isshiki's rods get repelled, he can shrink & store them back and re-attack Sasuke with them well before the 5-second cooldown is over. It's so easy for Isshiki to make Sasuke waste his ST/BT uses. He can just start to drop a single object to make Sasuke waste one use of ST, and attack Sasuke with multiple objects subsequently afterwards.
As for getting hit by ST, Killer B (base) did just fine after Nagato used a powerful one — all Isshiki needs to do is brace himself and since he can levitate, there is no need for him to dig anything into the ground like Six-Tailed Naruto did — he can leverage himself in mid-air.
2. Core-less CT was overpowered by Momoshiki in the anime, and assuming Isshiki gets tagged, he would have no trouble breaking free as well.
3. Ningendō only quickly worked on fodders far weaker than the user. Heck, Nagato was superior to Naruto, and still, it was taking time for him to pull Naruto's soul out. In this particular case, where Sasuke is facing someone with more chakra and physically superior to himself, the moment he tries to grab Isshiki, he gets punched to the face.
4. Genjutsu was not employed against Kaguya, Naruto, and Momoshiki either. Honestly, I think that if it was worth trying, Sasuke would have done so.
----
Naruto not using Kairiki Musō is a great point though. He should have definitely tried it.
I personally think however that either Isshiki can simply shrink the steam coming out of Naruto's body to cut off the boost or he can just shrink himself to avoid getting punched.