If you work for an organization funded by an organism you want to donate money to (e.g. an ea fund, Open Phil, ...), is asking for a lower pay a better way to donate money than giving money to the funding organism directly ?

The main advantage is that it removes the overhead when money loops around (taxes, some HR variable costs, ...).

The main disadvantage is if the org uses this excess money to fund activities below the funding bar of the funding organism. This can probably be assessed on a case-by-case basis based on how much you think your org is doing valuable work with marginal dollars relative to other orgs, and what's the policy of the org when it has unused funding.

It seems to me that in many situations, especially for very well payed for roles, the first consideration often outweighs the second one.

Did I miss any major consideration? For example, is this kind of practice bad for community health?