It is entirely possible to be political without being partisan. It is even demonstrated in a sense in the instances of harassment being discussed.
The groups in question have laudable goals in fields that are directly affected by government policy/action or lack thereof. Therefore interaction with government is often crucial.
It’s perfectly legal for these agencies to lobby government, work with or in opposition to government on a policy basis.
They do so, without regard to who is in power, or rather, with whomever is in power.
The government in question harasses them with audits from a compromised arms-length agency.
That demonstrates ideologue partisan behaviour on the part of the government, not on the part of the non-profit.
As I believe is stated elsewhere, the proof is in the pudding, these agencies are not losing their status because that would be easily contested, even beneficial, Streisand-style.
The birdwatchers in question sent two letters to sitting Ministers, regarding what is obviously a legitimate ancillary concern of any birdwatching society, preservation of ecosystem. Without bees, there’s no fucking birds to watch. Plain as the nose on my face. So that satisfies one condition, that their political activities be directly or demonstrably incidental to their primary purpose as a registered charity.
The only other condition is around their disbursement quota. Basically, how much of their $$ are they allocating for political purposes. From the information we have, they spent about Two Dollars on this particular political crusade. Possibly Less, since you can send a letter to some government addresses without postage.
Unless the letter said “we are spending X to try and XX” where XX is political or not in support of their primary purpose, it is readily apparent that the government is harassing them, because the PM, PMO & Cabinet are so stupidly ham-fisted that they believe anyone that questions them or incidentally opposes their unstated goals is acting in a partisan manner.