They say so in the article but you need a teensy bit more to make the connection. Here's the ELI5 version and then a link to too much detail:

You can have a Th1 or a Th2 reaction. One produces one kind of reaction and the other produces a different kind of reaction. And they both inhibit the other. It's a mechanism whose purpose (to the degree purposes exist) is to identify which kind of problem you have and apply as much energy as possible to that because they each fight different kinds of enemies. You'll see in the article they say:

> Allergic reactions are caused by a type of immune response known as Th2 response. Unvaccinated mice showed a strong Th2 response and mucus accumulation in their airways. The vaccine quelled the Th2 response and vaccinated mice maintained clear airways

Neither of these are immune (haha) to causing problems. Th1 was historically associated with multiple sclerosis. Obviously if your detection mechanism is broken you will create more and more of the wrong kind because of the fact one kind can beat the other with numbers but also because the wrong one won't even get the mis-detected enemy (which might not even be an enemy - and be harmless) out.

The too-much-detail: https://pmc.ncbi.nlm.nih.gov/articles/PMC27457/

> Th1-type cytokines tend to produce the proinflammatory responses responsible for killing intracellular parasites and for perpetuating autoimmune responses. Interferon gamma is the main Th1 cytokine. Excessive proinflammatory responses can lead to uncontrolled tissue damage, so there needs to be a mechanism to counteract this. The Th2-type cytokines include interleukins 4, 5, and 13, which are associated with the promotion of IgE and eosinophilic responses in atopy, and also interleukin-10, which has more of an anti-inflammatory response. In excess, Th2 responses will counteract the Th1 mediated microbicidal action. The optimal scenario would therefore seem to be that humans should produce a well balanced Th1 and Th2 response, suited to the immune challenge.

> Many researchers regard allergy as a Th2 weighted imbalance, and recently immunologists have been investigating ways to redirect allergic Th2 responses in favour of Th1 responses to try to reduce the incidence of atopy

There's a lot of detail to it. After all, it's an emergent evolved device that we carry, but that's the rough shape of it. You can create one kind of immune response and simultaneously shut down another kind.

Allergies are not simply overactive immune response. It’s the wrong type of response. What’s really intriguing is how much we can do innate immunity that we have done relatively little with.

I'm pretty allergic most of the time (lots of birch cross allergies and dust mites), but sometimes when I'm sick the allergic reactions appear to go down. Allergies can be pretty weird.

I would speculate it's something like, if your innate immune system is running "hotter", it's going to reduce the amount of time it takes to clear anything it runs into, leading to less time spent inflaming anything, in a similar fashion to how it significantly reduced viral payloads, leading to negligible symptoms when the adaptive immune system batted cleanup.