Should large capital expenditures like that be funded as explicit parts of the grants that use them (like an amortized user fee), or as items requesting funding on their own? You would think such things would deserve their own approved budgets (for the funders) and not be absorbed into a hard-to-dissect overhead factor.
The problem for large capital expenditures is they will last well beyond the grant, but they need to exist in order for the grant to be done. But a lot of funders don't want to pay for things that will last well beyond the project they're paying for. Indirects are one way to do this. Large capital acquisition grants are another.