My guess was that it is a way of keeping the organization from failing the public support test (https://www.irs.gov/charities-non-profits/exempt-organizatio...), which generally requires that at least 1/3 of the organization's support comes from the general public, not from, eg, one individual donor. Failing the public support test would make the foundation a private foundation instead of a public charity, which would change a number of regulations and have a small (usually 2%) on investment income.

What's particularly odd is that, if they were they a private foundation, as Acton is a board member (who also appears to have sole power to determine board members), I think the loan itself would be a prohibited act of self-dealing.

Might have also been an attempt to appear less of a target for that breed of self-serving administrators that seem to haunt certain other foundations in tech. And to keep reasonably humble people reasonably humble.