With regards to the gear upgrades, this is the general formula that FFXIV has had for a while. When Savage is released during even-number patches (3.0, 3.2, 3.4, 4.0, 4.2, etc.), the only gear available is the Savage gear and the unaugmented Tomestone gear, which can only be upgraded to the Augmented Tomestone gear by doing Savage. The tomestone weapons are only upgradable by clearing the third floor of a raid, and the final floor will always drop a better weapon. For odd-number patches (3.1, 3.3, 3.5, 4.1, etc.), they always have served as a “catch-up” patch when non-raiders could obtain upgrade pieces for their gear (save the weapon) by running the weekly 24-man, as well as alternative pieces of gear for their main jobs or alt jobs. The weapon upgrades have always been made available for the 24-man token exchange usually in a small x.18 patch following the release of the main catch-up patch.
I would still recommend attempting the later floors, because they are still worthwhile and for more than just mounts and glamour. The best gear for many jobs will rarely ever be “all Savage gear” or “all tomestone gear”, but rather a mixture of the two. The Savage weapons will always be the best just because of the weapon damage and main stat difference unless the secondaries are completely horrendous compared to the upgraded tomestone weapons.
People will still be running both Savage and Shinryu for gear for alt jobs and for tokens/pages and for the mount. But, sadly, if you are wanting “true progression” with regards to these fights, the best time to do them would be closer to when they are released. It’s much easier to get decent prog/learning groups for them compared to later in the tier, when a lot of people either just want strictly farming groups, or have already finished with Savage or the Extremes and have stopped running them.
There are rewards for clearing V3S+. People that cleared before catch-up patches probably feel like they were rewarded more than people who cleared during the catch-up patch do, but that doesn’t mean that the rewards aren’t still there. Whether or not something is “rewarding” though, is something only you can decide.