Not having the opportunity to lose them removes all uniqueness and value that finding them would bring.
This statement is false.
Even in Elden Ring, the game at hand, there is a counter example. If you miss Ranni at the first grace, the summoning bell shows up in the shop. Would it be a better game if it didn't, and you were permanently locked out of summons because you never went back to the first grace? No. No it would not. It remains unique and valuable.
Was my playthrough of FF7 enhanced because I didn't find the ribbon in the temple of ancients? Not especially. Was it further ruined because you can get one much later? No.
How are you supposed to build intrigue or mystery day one of release if nothing is hidden?
I'm not advocating for "nothing is hidden".
Let's consider some scenarios.
A Baldur's Gate 2 style RPG. There are many locations you can travel to on the world map. There are several party members you can recruit, where they play roles in your party and the story. You cannot create your own party members.
Scenario A:
If you return to location B between Chapter 3 and 4, you will find a wizard. He joins your party. There are no clues indicating you should return to location B. The story in fact guides you towards location C to advance the story.
Option 1:
If you do not visit location B during this narrow window of time, the wizard is gone forever. He never joins your party. His role in combat and narrative remains unfilled.
Option 2:
If you visit location B during this narrow window of time, the wizard joins your party. However, if you do not, he moves to another location as is appropriate for the story. If you find him earlier, you enjoy the advantages of the wizard earlier. Finding him later may have other disadvantages, such as him starting with a less favorable opinion or requiring resources to recruit him.
I feel like you think Option 1 is better. I think Option 2 is far superior. You get to reward people who are lucky or diligent, and everyone else doesn't get completely stiffed. Having the wizard show up now or later doesn't really impact the intrigue or mystery.
FromSoft games are often like this. You can meet NPCs earlier or go find loot sooner, but it rarely does a "You didn't do this exact thing at this exact time, so now you irreparably miss out." If you miss the ember in the depths, you can always go back and get it.
There are some things in the FromSoft games that you kind of have one shot at. Mostly the fixed NPC invasions. Those don't really bother me though since they're not that big a deal to miss.