As far as I've been able to find, there's nothing in the rules that states infused items (those created using infused reagents during daily preparations) have an effective level equal to your level. This is a massive oversight, which severely impacts the effectiveness of things such as poisons with the incapacitation trait. Adding someting similiar to the following into the next errata would clear up a lot:
Infused alchemical items you create during daily preparions have the following benefits: You may change the save DC for alchemical items created using infused reagents to equal to your class DC, and their effective item level is equal to your level.
If infused items had an item level equal to your level, you would never be able to use additives.
Technically it wouldn't affect that since the finish product would have it's level adjusted, not each individual ingredient, but yeah. Should have added "with respect to the incapacitation trait."
The only area I can think of where the Item Level would count for much would be counteract checks like with Sinew-Shock Serum. The Poisoner Research Field lets you change the DC of *any* Infused poison (including ones created with Advanced Alchemy) to your Class DC (if higher) and if you want Crafted poisons to be nastier you can take the 10th Level Feat Potent Poisoner.
The Powerful Alchemy class feature really ought to apply to Advanced Alchemy as well as Quick. It would help Bombers out a lot (Tanglefoot Bags especially.)
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There's actually quite a few items where level matters. Sinew shock is the obvious one, but we also have stuff like higher level antidote and antiplague. Lethargy and stupor poison both have incapacitation, and poison in general is harder to counteract if it's heightened. Even if it was a feat , I'd probably take it on my toxicologists