for me i almost always play with rymrgand's challenge, so there's a real cost to rest-spamming. both monetarily (have to keep replacing food) and also because i can't stock up on good rest bonuses so i end up with lame rest bonuses (if i haven't been paying attention to how long i've been at sea i might literally just be left with water and hardtack). so it's not quite a no-rest challenge, but there's friction that can be a necessary counterbalance for on-rest vs on-encounter abilities.
more generally the on-rest mechanics of this game are kind of a poor fit. most of the game is geared around encounters and trying to avoid the tedium of skill resource management between fights, and between empower points and the growing amount of items they added that had on-rest effects, there's a gameplay design tension. generally i'm in favor of the idea that we shouldn't have on-rest effects at all, but in practice i think that would be a huge power creep.
outside of generalizations, the trinkets come so late that i'm not sure how much of a harm making those per-encounter would actually hurt the game balance. i actually ended up having lots of fun with the merge trinket from hauane o whe and the fiery core trinket from dorudugan, but at that point there were only like... 6 encounters in the game left, some of them extremely easy, so i ended up using it only like two or three times. would've been nice to have them up in every battle, and i already had to kill megabosses not sure i should be worried about encounter balance for some extremely under-leveled faction/mainquest content.
edit: maybe instead of makin them per-encounter, they are multiple uses per rest? i'm just thinking of leaping boots, i really like that item, and 2 uses/rest hit a sweet spot where i didn't feel like hoarding the ability, but i still had to be a little careful with it.
edit also to add - the unique amulet you get from assembling across the three DLC really should be per-encounter. a 20s dominate can be pretty powerful, but as a payoff for three DLC, and an amulet slot, and the fact that you can miss with the dominate, really makes it feel underpowered for one/rest usage.