The difference is that when this happens to a private organisation, it's not the taxpayer footing the bill.

Why does that matter? The process of budgeting is the same in public and private organizations, including the unpredictable elements that result in overestimation and padding. The source of funding doesn't affect that. Federal government expenditures are only indirectly related to tax revenues in any case.

It matters because if it happens to a private organisation that does not affect the average Joe. It's when it happens to governmental organisations that it matters because it means increased taxes and/or decreased useful public services.

It does affect the average Joe, because Joe is buying the products or services the private organisation creates. If Walmart, to pick a random example, has this phenomenon and spends extra money wastefully at the end of their financial cycle, that would mean that every product Walmart sells has to cost a bit more to pay for that, and Joe's monthly grocery bill goes up.

Thankfully Joe has many other options than Walmart. But you only get one government.

You can vote on your government and you can move to a different country.

For average person it's easier to change the government than to change Google CEO.

No, it's a customer who'll be footing the bill. Sometimes that customer can go somewhere else, sometimes not (eg. Internet providers in the US)

If private organisations are doing it then it must be good, otherwise they would go bust when other large companies don’t do it and can undercut.