It's an open secret that the indirect costs are budgeted to make profit for a university. That is, the stated costs exceed actual costs. This has been publicly discussed by former federal division heads in major outlets.
The problem with this is the universities rely on this funding to stay afloat, so there's a tail wagging the dog problem. Basically the evaluation of scientific merit then derives from a decision as to whether or not it can procure money from the federal government.
That in turn is driven by all sorts of factors:
https://journals.plos.org/plosone/article?id=10.1371/journal...
I don't want to argue that grants are bad but I do think the system is broken. Everyone passes the buck to the federal government in this kind of shell game, and then the federal grant system becomes the [near] monopoly over scientific decision making.
The analogy I tend to use in my head is that it's like if your state gave out grants to fund plumbing projects, and people realized that these grants paid more than the actual costs for the project. You have a plumbing project, get the plumber to get a grant for you, and pocket the difference. So people stop hiring plumbers on the basis of the work they do per se, and instead hire them on the basis of their ability to procure state grants. That's kind of what the system works like now.
Do industry grants have larger overhead? It doesn't matter one way or another. That's a different issue. Two wrongs don't make a right either.