There are some glaring issues with a few Alchemist abilities, most of which seem to stem from certain parts of the rules failing to be updated when other dependent systems changed from the playtest.
At level 13, The Alchemist's Mutagenist field gives you the ability to benefit from multiple mutagens at the same time, but the caveats seem to be based on the playtest version of mutagens, where drinking a new one would override the other while maintaining the drawbacks of both. In the final version of the rules, mutagens have no such language, instead functioning as normal polymorph effects with no mention of drawbacks from multiple mutagens persisting.
This leads to a new problem, though, as according to page 301, if someone comes under the effect of a new polymorph effect while already benefiting from one, the new effect attempts to counteract the second. This is straightforward with spells, but there are no rules to handle how an item attempts a counteract check. What modifier and proficiency bonus would you use for such a check?
The issue of items attempting counteract checks also comes into play with the Merciful Elixir feat. It specifies that the item itself attempts the counteract check, but does not explain what modifiers are involved. Even if the Alchemist is supposed to be the one making the check, it's still missing language about what sort of check to make. What modifier? What proficiency bonus?
The language is the same for spells and items.
The language used is "the spell/item/effect tries to counteract"
The general rule is that you use the relevant skill or ability modifier.
In this case it would be the Crafting Skill of the one who made the item trying to counteract.
What it can counteract then goes by the level of the item vs the level of the effect.
As for Mutagenist, it's pretty straightforward :
"you can gain the benefits and the drawbacks of both mutagens at once, despite the fact that they both have the polymorph trait and would not normally function together."
So basically, ignore the polymorph restriction of one trying to counteract the other.
As a GM, I would certainly rule that the counteract check uses the creator's crafting skill, but it still needs clarification, as there's no clear way to determine what the "relevant skill or ability" is. That also doesn't really cover issues of drinking purchased or found mutagens (though that's probably going to be a rare occurrence).
As for the Mutagens, the rules make sense as written. They're just not consistent with the way the mutagen rules are presented in the Alchemical Items chapter, but instead seem to be based on an older version of the mutagen rules not present in the final book.
Everything in the level 13 ability certainly works as written, it just leads to a strange case where, prior to getting that ability, the mutagenist can drink a mutagen to override a previous one (drawbacks included), but once they hit level 13, doing the same will now stack up multiple drawbacks and only override the benefits.
It seems unlikely that this ability is intended to change the way mutagens work back to their playtest functionality, and coupled with the research field's reference to playtest mutagen rules in its initial abiltiy, it looks like either
A) some of the mutagen rules were accidentally cut from the final book, or
B) The mutagenist was not updated properly to account for mutagens changing in functionality.
Either way, I think that warrants clarification.
It clearly states that you keep BOTH benefits and negatives despite the polymorph trait.
So I really don't see an issue here.
And yes, before the ability you can override one Mutagen with another.
For counteracting it states that you use the "relevant skill". So it's pretty raw that you use the craft skill since that's the relevant skill for an item.
Like the casting l is what produces a spell effect, similarly the crafting is what produces an item.
I agree that RAI the relevant skill would be crafting, but I don't think it's clear RAW. Every other counteract check clearly lists what modifier you use. The absence of this one suggests that something is missing.
My confusion with the mutagenist is, again, that it very clearly seems to be written referencing playtest mutagen rules (in two different abilities), but the final mutagen rules lack many of the limitations of the playtest. Why does the level 13 ability apparently make all drawbacks stack (something mutagen drawbacks did in the playtest) when mutagens no longer do that? Why does the initial field ability say that you can benefit from mutagens not brewed for you, when that limitation is not preserved from the playtest?
While I agree there's a ton of leftover garbage from the playtest (the level 1 ability to start with...), the stacking issue is clear:
By default, since it says nothing different anywhere, without the mutagenist ability they are simple polymorph effects:
You have one set of bonuses/penalties. If you come under the effects of another polymorph, they attempt to counteract. That applies to the whole effect (both bonuses and penalties)
The mutagenist ability changes this interaction to ignore the polymorph trait. So you get both benefits but also both penalties.
That part imo isn't ambiguous at all, "you gain both benefits and penalties disregarding the polymorph trait" is as straightforward as it can get.
As for the counteract, while it doesn't say specifically what to use, it gives the general rule for all counteract effects. And the general rule is "use the relevant skill or ability". So it falls under the general blanket.
I don't think anything's ambiguous. I understand how the ability works and how two mutagens would stack. It's just that, in light of the leftovers seen in the first level ability, it looks like the level 13 ability suffers from the same issue.
If you come under the effects of any further mutagens while benefiting from two mutagens, you lose the benefit of one of the former mutagens of your choice, while retaining the drawbacks of all the mutagens.
As written it appears to revert mutagens back to their playtest rules (because it reiterates those rules). With that ability, when you take a third mutagen, it overrides one previous mutagen but all drawbacks stay (including the drawback of the overridden mutagen). You are then suffering from two benefits and three drawbacks. Take a fourth and you now have two benefits and four drawbacks. Suddenly all drawbacks stack again like they did in the playtest.
That seems unintended. Instead, this seems like an oversight where a rule failed to be properly updated when a dependent rule changed.
I will admit that perhaps this issue doesn't belong in the rules forum though, as it's not really a question of how things work as written, but I'm not really sure what the proper forum would be then.