I guess there is no real alternative to SetTracker.
Maybe WishList is a helper here too for set items you are searching.
FCOIS ca be of use here as you can define your own marker icons (dyanmic ones, up to 30) and set what the name and look will be.
Apply it to your set prts once and you are fine.
You can even automatically let the addon mark your set parts (independent to the set name!) by help of their trait with different marker icons. e.g. mark divine and infused ones as major set parts and sturdy ones for tank, others for healers.
If you mark the dynamic icons as "Use as gear set icon" you can easily mark all equipped items with 1 click (if enabled in the settings) with the same marker icon (e.g. a dynamic icon named "Heal 1").
You can use the filter buttons to only show these items in your invenmtories, banks etc.
+the items are always protected they way you want themt o be protected:
No destroy, no deconstruction, no trade, no sell, no imrpove or allow improve, no mail, etc.
It needs some time to setup the addon the way you like it to be but it's a great help if you also use addons like DoItAll to mass deocnstruct etc. so all important items will be kept without the worry they will be lost or destroyed somehow + you can easily filter the items in combination with other addons like AdvancedFilters BETA and FCOCraftFilter in your inventories + crafting tables.
Check the FAQ for FCOIS for some help and examples:
https://www.esoui.com/portal.php?id=136&a=faq
Edit:
FCOIS gopt SetTracker support as well but this will only read the defined sets in SetTracker and mark the items in your inventories with FCOIS marker icons, so you can protect and filter them.
It's basically the same as doing this manually "once" for the set parts (as they will be remembered for all your chars then if you use account wide settings) or using the automatic set marking of FCOIS.
Not sure what you mean by bloat of uniqueIds and interfere here though?