How to make Signet not retarded gameplay-wise:

Add a downside to it
Make it give you a DoT to HP/MP while you are in a battle, make it give you less or 0 XP, make it temporarily reduce your level while you have it on, SOME kind of point to making it an opt-in thing.

The newest Zelda game has items you put in your adventure pouch that increase the drop rate on certain items. You have to talk to a NPC to put them in your pouch. The reason that this is a meaningful gameplay decision is that this pouch is also where you hold your potions/ammo bags so you risk running out of supplies or not being able to heal yourself because you wanted more money drops.
Make it limited, but powerful
Let us only use it once a week for an hour, for example, but give us a ton of seals during that time. Alternatively, let us use it once a day for less seals. In the end this basically would just become another version of guardian aspect.
Make it permanent
We already have ourselves pledged to a Grand Company, we can't pledge to more than one, so just cut the bullshit and let all our actions from then on be counted for whatever sort of conquest system that may get added, without having to get a buff. We don't have to worry about refreshing buffs, we don't have to needlessly talk to NPCs, and it adds more substance to our joining a Company.

FYI this is how it should have been handled in 11 too. You could only be allied with one nation so Signet should have been permanent. Sanction/Sigil should have been permanent with you just going to a NPC to change your bonuses. Eventually you ran into the problem where you had the wrong buff for the wrong zones which was annoying and just making everything permanent and not tied to a buff would have rectified that issue.