The Good
We have a reason to spend a lot of raid currency in a nice and incremental way. More reason to chase raid currency means there is a reason to keep running any recent raid. This keeps regular players engaged and helps the more casual people with being able to find groups.
The mixing and matching of filigree sets is more interesting/fun with multiple dual raid filigrees.
There's a mild economy for raid and rare filigrees.
The "Bad"
The current situation doesn't fit what was originally envisioned on a SSG whiteboard.
An embarrassing edge case in coding is on full display with the current system.
Wait That's Illegal
Instead of spending even more time with what appears to be a problematic and tricky system, leave it alone for now and redesign it instead.
Make sentience something more like the enhancement tree systems.
This would alleviate developer stress related to wanting to create weapons that are situational and fun but not best in slot. Players benefit from being able to swap weapons again and chase extra fun toys while still retaining regular bonuses.
Players would even be tempted to rez scroll their friend instead of carrying them while waiting to spend 2 boosts or 800 spell points.
Since storage and toolkits are the monetary backbone of the system, the retrofit can still have filigrees that slot into the trees to give varied bonuses.
While you're at it allow us to pay some sort of currency to upgrade any filigree into its rare version.
Keep the current raid rune+upgrades.
Create dedicated "no rules" slots that allow us to double/triple/quadruple up on specific filigrees.
Allow sentience in a level-gated way from low levels. Potentially even level 1.