Version: 1.3-rc-20221213

How to reproduce:

1. create a pattern for Nether Quartz/Certus Quartz/Fluix seeds (and place it in the interface used for crafting)
2. create a pattern for corresponding Pure Crystal
3. ensure there are no corresponding seeds in the storage
4. try to craft the Crystal

What happens:
AE2 does not see the pattern for the seeds.

Similar issue happens when crafting Pure seeds (as part of some higher-level craft), assuming you have set up a process for this using Level Emitter with Crafter Card set to "Emit to craft" (cause direct pattern does not work as it does not see the seeds): AE does not see existing Pure Crystals in storage. It crafts new ones instead (though manages to see them and use in further craft).

I'm not quite confident in MC mechanics, but the problem somehow lies in difference betwee what item is in JEI (and thus gets to the pattern), and what item is "physically" produced (so is in your inventory). As for the seeds, it is still possible to craft them on-demand using also a Level Emitter with Crafting Card, just set the "filter" not from JEI, but directly from your inventory.

It sounds like there is an NBT mismatch between the imported recipe from JEI and the actually created item.

Please try this: manually craft the desired item once, then modify any patterns using the bad copy from JEI by clicking away the ghost item (from the inputs or outputs of the recipe) and using the crafted item to put it back into the pattern.

The workaround you described for crafting seeds should be unnecessary.

Thanks. That's what I did initially, and thought I did all substitutions, but only now I rechecked again, and finally came to decently working variant.

In other words:

1. I made processing patterns for seeds (because direct craft does not allow substitution of final result from inventory); those patterns are used in Interfaces placed along with Molecular Assemblers. But it's worth noting, that Assemblers themselves also need to have corresponding patterns (but in this case pattern can be a usual craft-pattern from JEI), so that Assembler still knew what to craft.
2. patterns for Pure Crystals are also made like a process, and all the items (Seed as input and Crystal as output) are set from inventory. They are used, obviously, also in the Interface beyond the Growth Chamber (with Item Conduit sucking the results back to the interface).

I checked this by creating another arbitrary pattern involving Pure Crystal, and this time it successfull managed to "find" all underlying recipes.

Did you try to make Pure Crystals without having seeds already in storage? In the video, you already have 2 of each.
UPD: Also, try to make another pattern which needs any of Pure Crystals, and try to craft it in 2 scenarios: when you already have some, and when you don't.