Adjusting depreciation schedules are very typical tax strategies for businesses. Hell, I've done this for a one-man shop making less than $100k in a year. Depreciation strategies are an important part of cash-flow management for capital-intensive industries. Otherwise, it's almost impossible to start a factory or other large industrial firm. Cash flow is marginal compared to capital, but the tax rate is proportional to capital. You can easily be put in a situation where the tax burden exceeds the free cash of the business.

I guess I'm not clear on what detail you think is missing. To me, their objections and actions are very clearly worded.

I believe they pointed out that they regularly pay taxes, that the tax rate for that year was due to accelerating depreciation, and the NYT is engaged in the same accounting strategies.

Accelerating depreciation has no net tax benefit over the full depreciation period. If the depreciation period is 10 years, but they accelerate in the first year, their net tax rate is the same over the 10 years as if they did not accelerate. They are simply moving their tax burden to the future.

They also took other current expenses to charge their pension, but again, these are expenses that they cannot take in the future - they will pay additional tax on future incomes. The net is the same.