Although I am not familiar with the specific details of the FedEx plan, there are other very plausible scenarios beyond the ones that you correctly identified that could easily explain how a defined benefit(DB) pension fund could get upside down over time.
1a. Many DB plans were set up with the assumption of growth in terms of an ever increasing number of people participating, read making contributions to the fund, in the plan. When any industry overall ceases to grow, or a particular company in said industry ceases to grow, and then people start retiring and drawing benefits and the number of "new" workers making contributions is not enough to keep up then the health of the fund drops.
1b. Corollary - It is possible too that simple demographics could be at play here too. There are many more Boomers, now retiring left and right, than there are in the subsequent generation, Gen X. This is just a reality and one that is impacting retirement vehicles such as pensions EVERYWHERE. See link below.
https://www.statista.com/statistics/797321/us-population-by-generation/
2. Straight up fraud. Again, I don't know the particulars on the FedEx plan, but this has happened plenty of times and plenty of places and often then leaves the future health of the fund in a figurative straight jacket.
3. Perhaps this fits under your #2 or #3 above, but the contribution rate and corresponding payout formula are often the result of labor negotiations and let's just say that there are no guarantees that wise, long term decisions are always made when management and labor are locking horns. Sometimes things are agreed to now, that will certainly lead to problems in the future, but they happen anyway.
I don't think these additional potential reasons are an exhaustive list either FWIW, but all of the above are not without precedent in the world DB plans. I would suspect that there is some combination of the above factors at play here.
Also, not all that many years ago there were changes to the federal tax code that now obligates companies to show their pension liability in their financials. This can be a gigantic stumbling block when said company then say...goes out for additional financing and the prospective lenders say WHOA, what's this giant liability here...no loan for you.